Case 1 (A.1.NmC2): PP431249.1




Target: 83 samples           Number of changes: 42                                                            


BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 28-29, 37-38                  BC BR coord: 6055 - 6056, 9295 - 9296


Direction L1: >>             Initial region span: 1-28,29-37,38-42Gap history (edge excluded): 28-38 ->


Alt. candidates: [], []                                                                                              


Model 1BP/2BP comparison:    2BP vs 1BP: 3.55e-03                                                                    


Rec. model vs L1: 3.55e-03   Rec. model vs L2: 2.28e-26                                                       


Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 28 28.439834 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 29 0.829987 NaN NaN NaN * * *
A.1.NmC2 83 38 0.000000 -5.810408 53.620815 1.307027e-03 *
A.1.NmC1 181 38 -1.197639 -37.418671 116.837341 2.444759e-17
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 38 4.270669 None None None * * *



Target sequence

, 254_A|G, 428_T|A, 755_T|C, 875_C|T, 881_G|T, 923_G|T, 1265_A|G, 1398_C|T, 1616_C|T, 2375_C|T, 2534_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3080_T|C, 3140_A|G, 3186_G|A, 3218_T|A,
3332_G|A, 3459_C|T, 3534_G|A, 3731_C|T, 3911_A|G, 3989_T|C, 5651_C|T, 5937_T|C, 6008_C|T, 6545_C|T, 6908_T|C, 6983_A|G, 7064_T|C, 7451_A|C, 7633_T|C, 7805_T|C, 8250_C|A, 8474_C|T, 9296_C|T,
9305_C|T, 9353_T|C, 10164_A|G, 10561_T|C
 Case 2 (A.1.NmC1): MT377503.1




Target: 181 samples          Number of changes: 155                                                                   


BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 9-10, 102-103                  BC BR coord: 814 - 815, 6580 - 6581         


Direction L1: <<             Initial region span: 1-9,10-46,129-155Gap history (edge excluded): 9-129 -> 46-129


Alt. candidates: [], []                                                                                                      


Model 1BP/2BP comparison:    2BP vs 1BP: 1.09e-21                                                                            


Rec. model vs L1: 2.96e-41   Rec. model vs L2: 4.67e-33                                                               


Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 9 3.359009 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 46 0.784264 NaN NaN NaN * * *
A.1.NmC2 83 10 0.000000 -729.844073 1695.688146 8.096071e-310
A.1.NmC1 181 10 -1.832966 -66.399428 368.798855 1.093394e-21
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 129 21.721407 None None None * * *



Target sequence

, 254_A|G, 423_G|A, 455_G|A, 467_T|C, 479_G|A, 523_A|G, 558_T|C, 653_G|A, 803_A|G, 884_A|G, 974_C|T, 1115_T|C, 1175_A|G, 1211_T|C, 1370_G|A, 1616_C|T, 1718_C|T, 1745_G|A, 1896_T|C, 1902_A|G,
2060_T|A, 2066_C|T, 2178_C|T, 2207_A|G, 2225_A|G, 2333_T|C, 2375_C|T, 2411_C|T, 2519_G|A, 2525_G|A, 2555_T|C, 2576_G|A, 2606_C|T, 2648_T|G, 2654_C|T, 2724_T|C, 2726_G|A, 2756_T|A, 2819_G|A,
2846_G|A, 2925_G|A, 3014_T|C, 3038_T|C, 3041_T|A, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3266_C|T, 3332_G|A, 3350_G|A, 3518_C|T, 3534_G|A, 3641_C|T,
3731_C|T, 3885_T|C, 3989_T|C, 3992_C|T, 4085_T|C, 4106_A|G, 4238_C|T, 4286_C|T, 4295_A|G, 4319_G|A, 4454_G|A, 4493_C|T, 4523_G|A, 4595_C|T, 4652_A|G, 4733_T|C, 4790_A|G, 4850_C|T, 4952_C|T,
4994_G|A, 5000_T|C, 5030_C|A, 5060_T|C, 5177_G|A, 5198_T|C, 5267_T|C, 5279_A|G, 5324_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5546_T|C, 5591_T|C, 5612_T|C, 5744_A|G, 5828_T|C, 5937_T|C, 6056_C|T,
6101_T|C, 6155_A|G, 6164_C|T, 6275_A|T, 6470_G|A, 6473_T|A, 6684_A|C, 6807_T|C, 6890_A|G, 6911_C|T, 6983_A|G, 7037_C|T, 7050_T|C, 7079_A|G, 7290_G|A, 7451_A|C, 7517_C|T, 7574_C|T, 7633_T|C,
7713_T|C, 7784_G|A, 7805_T|C, 7817_G|A, 7887_T|C, 7931_T|C, 8007_G|A, 8105_C|T, 8408_T|C, 8516_A|G, 8606_C|T, 8630_AA|GG, 8696_C|T, 8924_G|C, 8927_G|C, 8930_G|A, 8932_C|A, 8939_G|C, 8991_C|T,
9017_T|C, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9503_C|T, 9509_T|C, 9527_A|G, 9612_T|C, 9728_A|G, 9752_G|A, 9809_C|T, 9953_A|G, 10004_T|C, 10163_T|C, 10184_C|T, 10208_G|A, 10289_G|A,
10392_A|G, 10477_T|C, 10561_T|C
 Case 2 (A.1.NmC1): KY241700.1




Target: 181 samples          Number of changes: 136                                                            


BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 41-42, 87-88                   BC BR coord: 4060 - 4061, 4453 - 4454


Direction L1: <<             Initial region span: 1-41,42-87,88-136Gap history (edge excluded): 41-88 ->


Alt. candidates: [], []                                                                                               


Model 1BP/2BP comparison:    2BP vs 1BP: 2.48e-27                                                                     


Rec. model vs L1: 2.64e-28   Rec. model vs L2: 1.55e-119                                                       


Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 41 48.007145 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 42 6.214385 NaN NaN NaN * * *
A.1.NmC2 83 87 -1.192791 -442.187130 978.374260 1.829592e-195
A.1.NmC1 181 87 -1.972447 -55.045602 204.091204 2.483820e-27
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 88 67.370279 None None None * * *



Target sequence

, 254_A|G, 272_A|G, 523_A|G, 558_T|C, 653_G|A, 803_A|G, 815_A|G, 1175_A|G, 1238_C|T, 1241_T|C, 1304_C|A, 1406_T|C, 1616_C|T, 1865_T|C, 1991_T|C, 2192_C|T, 2375_C|T, 2405_T|C, 2525_G|A,
2654_C|T, 2681_G|A, 2724_T|C, 2732_G|A, 2799_T|C, 2925_G|A, 3032_A|T, 3059_G|A, 3070_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3254_T|C, 3332_G|A, 3377_A|G, 3518_C|T, 3534_G|A, 3731_C|T,
3899_C|T, 3945_T|C, 3989_T|C, 4061_A|G, 4067_T|G, 4076_C|T, 4079_G|A, 4083_T|A, 4085_T|C, 4097_T|C, 4103_G|A, 4106_A|G, 4112_C|T, 4128_T|C, 4130_A|G, 4152_C|T, 4154_A|G, 4157_C|A, 4167_C|G,
4169_G|A, 4172_C|A, 4178_C|T, 4181_C|T, 4184_C|T, 4190_G|A, 4196_G|A, 4202_G|A, 4238_C|T, 4244_A|T, 4253_T|C, 4268_C|T, 4272_T|C, 4277_T|C, 4286_C|T, 4298_T|C, 4301_A|T, 4313_G|A, 4322_C|T,
4325_G|A, 4328_C|A, 4331_TC|CT, 4346_T|C, 4349_C|T, 4358_A|G, 4412_A|G, 4415_T|C, 4439_C|T, 4445_C|T, 4448_T|C, 4454_G|A, 4457_A|G, 4520_C|T, 4523_G|A, 4733_T|C, 5000_T|C, 5060_T|C, 5245_A|C,
5288_C|T, 5375_A|G, 5387_C|T, 5636_A|G, 5675_T|C, 5744_A|G, 5937_T|C, 6056_C|T, 6104_T|C, 6363_C|T, 6410_T|C, 6506_A|G, 6581_G|A, 6684_A|C, 6983_A|G, 7050_T|C, 7451_A|C, 7517_C|T, 7633_T|C,
7652_C|T, 7805_T|C, 7860_T|C, 8007_G|A, 8312_T|A, 8408_T|C, 9017_T|C, 9305_C|T, 9353_T|C, 9434_A|G, 9440_T|G, 9455_G|A, 9500_T|C, 9728_A|G, 9752_G|A, 9809_C|T, 9953_A|G, 10208_G|A, 10289_G|A,
10392_A|G, 10477_T|C, 10561_T|C
 Case 2 (A.1.NmC1): KY241712.1




Target: 181 samples        Number of changes: 141                                                   


BC: A.1 + A.1.NmC1         BC BR: 21-22                    BC BR coord: 427 - 428            


Direction L1: <<           Initial region span: 1-15,66-141Gap history (edge excluded): 15-66


Alt. candidates: [], []                                                                                    


Model 1BP/2BP comparison:  -                                                                               


Rec. model vs L1: 2.09e-104Rec. model vs L2: 1.55e-06                                               


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 15 -7.435613 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 66 96.59115 None None None * * *



Target sequence

, 40_TT|CC, 50_A|G, 56_G|A, 122_A|G, 179_G|A, 181_G|A, 188_T|G, 191_G|A, 194_C|T, 204_C|T, 233_G|A, 242_G|A, 248_C|T, 254_A|G, 257_T|A, 272_A|G, 299_T|C, 302_C|T, 308_T|C, 320_A|C, 371_G|T,
523_A|G, 558_T|C, 653_G|A, 803_A|G, 815_A|G, 1175_A|G, 1238_C|T, 1241_T|C, 1304_C|A, 1406_T|C, 1616_C|T, 1646_A|G, 1655_C|T, 1697_A|G, 1701_C|T, 1709_G|A, 1739_T|C, 1757_T|C, 1769_A|C,
1781_C|T, 1784_T|C, 1796_G|A, 1825_G|A, 1831_C|T, 1841_C|T, 1865_T|C, 1967_A|G, 1973_C|T, 1991_T|C, 1998_G|A, 2000_T|C, 2005_CT|TC, 2027_A|G, 2030_T|C, 2045_G|A, 2049_T|C, 2060_T|C, 2069_A|G,
2072_C|T, 2093_T|A, 2103_C|T, 2108_A|G, 2114_T|C, 2129_C|T, 2192_C|T, 2375_C|T, 2405_T|C, 2525_G|A, 2654_C|T, 2681_G|A, 2724_T|C, 2732_G|A, 2799_T|C, 2925_G|A, 3032_A|T, 3059_G|A, 3070_T|C,
3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3254_T|C, 3332_G|A, 3377_A|G, 3518_C|T, 3534_G|A, 3731_C|T, 3899_C|T, 3945_T|C, 3989_T|C, 4085_T|C, 4169_G|A, 4328_C|T, 4454_G|A, 4520_C|T, 4523_G|A,
4733_T|C, 5000_T|C, 5060_T|C, 5288_C|T, 5375_A|G, 5387_C|T, 5636_A|G, 5675_T|C, 5744_A|G, 5937_T|C, 6056_C|T, 6104_T|C, 6363_C|T, 6410_T|C, 6506_A|G, 6581_G|A, 6684_A|C, 6983_A|G, 7050_T|C,
7451_A|C, 7517_C|T, 7633_T|C, 7652_C|T, 7805_T|C, 8007_G|A, 8312_T|A, 8408_T|C, 9017_T|C, 9305_C|T, 9353_T|C, 9434_A|G, 9440_T|G, 9455_G|A, 9500_T|C, 9728_A|G, 9752_G|A, 9809_C|T, 9953_A|G,
10208_G|A, 10289_G|A, 10392_A|G, 10477_T|C, 10561_T|C, 10721_C|A
 Case 2 (A.1.NmC1): PP626402.1




Target: 181 samples          Number of changes: 108                                                                 


BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 99-100, 104-105                   BC BR coord: 9751 - 9752, 10288 - 10289


Direction L1: >>             Initial region span: 1-99,100-104,105-108Gap history (edge excluded): 99-105 -> 


Alt. candidates: [], []                                                                                                    


Model 1BP/2BP comparison:    2BP vs 1BP: 1.05e-04                                                                          


Rec. model vs L1: 1.16e-06   Rec. model vs L2: 1.83e-101                                                            


Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 99 66.6587 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 104 0.547984 NaN NaN NaN * * *
A.1.NmC2 83 100 0.000000 -52.421981 124.843962 9.895125e-24
A.1.NmC1 181 100 -1.718788 -8.616938 37.233877 1.046384e-04 *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 105 5.321986 None None None * * *



Target sequence

, 254_A|G, 272_A|G, 281_A|G, 338_T|C, 437_C|T, 523_A|G, 536_G|A, 558_T|C, 602_C|T, 653_G|A, 662_T|C, 803_A|G, 942_T|C, 1175_A|G, 1241_T|C, 1367_C|T, 1430_G|A, 1487_G|A, 1616_C|T, 1739_T|C,
2030_T|C, 2375_C|T, 2432_C|T, 2525_G|A, 2654_C|T, 2681_G|A, 2724_T|C, 2732_G|A, 2879_T|C, 2925_G|A, 2969_C|T, 3059_G|A, 3106_A|G, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3228_T|C, 3254_T|C,
3332_G|A, 3534_G|A, 3731_C|T, 3989_T|C, 3995_C|T, 4085_T|C, 4307_G|A, 4328_C|T, 4400_C|T, 4454_G|A, 4523_G|A, 4607_A|G, 5000_T|C, 5060_T|C, 5192_C|T, 5375_A|G, 5387_C|T, 5456_G|A, 5636_A|G,
5744_A|G, 5828_T|C, 5918_T|C, 5937_T|C, 6056_C|T, 6185_T|C, 6227_A|G, 6363_C|T, 6575_A|G, 6581_G|A, 6684_A|C, 6728_T|C, 6981_.|G, 6984_G|A, 6986, 7050_T|C, 7224_T|C, 7409_A|G, 7451_A|C,
7517_C|T, 7633_T|C, 7751_A|G, 7763_C|T, 7793_C|T, 7805_T|C, 7820_A|G, 8007_G|A, 8217_T|C, 8360_A|G, 8408_T|C, 8711_A|G, 8789_T|C, 8978_C|T, 9017_T|C, 9305_C|T, 9353_T|C, 9398_A|G, 9434_A|G,
9440_T|G, 9455_G|A, 9728_A|G, 9803_C|T, 9812_C|T, 9824_T|C, 10159_C|T, 10262_T|C, 10289_G|A, 10392_A|G, 10477_T|C, 10561_T|C
 Case 2 (A.1.NmC1): MT377491.2




Target: 181 samples          Number of changes: 107                                                                


BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 98-99, 103-104                   BC BR coord: 9751 - 9752, 10288 - 10289


Direction L1: >>             Initial region span: 1-98,99-103,104-107Gap history (edge excluded): 98-104 -> 


Alt. candidates: [], []                                                                                                   


Model 1BP/2BP comparison:    2BP vs 1BP: 1.05e-04                                                                         


Rec. model vs L1: 1.16e-06   Rec. model vs L2: 4.91e-95                                                            


Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 98 64.719124 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 103 0.547984 NaN NaN NaN * * *
A.1.NmC2 83 99 0.000000 -52.421981 124.843962 9.895125e-24
A.1.NmC1 181 99 -1.718788 -8.616938 37.233877 1.046384e-04 *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 104 5.321986 None None None * * *



Target sequence

, 254_A|G, 272_A|G, 281_A|G, 338_T|C, 437_C|T, 523_A|G, 536_G|A, 558_T|C, 602_C|T, 653_G|A, 662_T|C, 803_A|G, 942_T|C, 1175_A|G, 1241_T|C, 1367_C|T, 1430_G|A, 1487_G|A, 1616_C|T, 1739_T|C,
2030_T|C, 2375_C|T, 2432_C|T, 2525_G|A, 2654_C|T, 2681_G|A, 2724_T|C, 2732_G|A, 2879_T|C, 2925_G|A, 2969_C|T, 3059_G|A, 3106_A|G, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3228_T|C, 3254_T|C,
3332_G|A, 3534_G|A, 3731_C|T, 3989_T|C, 3995_C|T, 4085_T|C, 4307_G|A, 4328_C|T, 4400_C|T, 4454_G|A, 4523_G|A, 4607_A|G, 5000_T|C, 5060_T|C, 5192_C|T, 5375_A|G, 5387_C|T, 5456_G|A, 5636_A|G,
5744_A|G, 5828_T|C, 5918_T|C, 5937_T|C, 6056_C|T, 6185_T|C, 6227_A|G, 6363_C|T, 6575_A|G, 6581_G|A, 6684_A|C, 6728_T|C, 6981_.|G, 6984_G|A, 6986, 7050_T|C, 7224_T|C, 7409_A|G, 7451_A|C,
7517_C|T, 7633_T|C, 7751_A|G, 7763_C|T, 7793_C|T, 7805_T|C, 8007_G|A, 8217_T|C, 8360_A|G, 8408_T|C, 8711_A|G, 8789_T|C, 8978_C|T, 9017_T|C, 9305_C|T, 9353_T|C, 9398_A|G, 9434_A|G, 9440_T|G,
9455_G|A, 9728_A|G, 9803_C|T, 9812_C|T, 9824_T|C, 10159_C|T, 10262_T|C, 10289_G|A, 10392_A|G, 10477_T|C, 10561_T|C
 Case 2 (A.1.NmC1): MG807647.1




Target: 181 samples          Number of changes: 109                                                                          


BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 100-101, 105-106                   BC BR coord: 9499 - 9500, 10163 - 10164        


Direction L1: >>             Initial region span: 1-100,101-102,106-109Gap history (edge excluded): 100-106 -> 102-106


Alt. candidates: [], []                                                                                                             


Model 1BP/2BP comparison:    2BP vs 1BP: 2.67e-03                                                                                   


Rec. model vs L1: 3.35e-05   Rec. model vs L2: 1.39e-44                                                                      


Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 100 23.420651 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 102 0.266565 NaN NaN NaN * * *
A.1.NmC2 83 101 0.000000 -41.455155 100.910310 3.358625e-18 *
A.1.NmC1 181 101 -1.634194 -7.145263 32.290526 2.671808e-03 * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 106 5.321986 None None None * * *



Target sequence

, 76_T|A, 254_A|G, 272_A|G, 437_C|T, 523_A|G, 558_T|C, 653_G|A, 746_T|C, 803_A|G, 942_T|C, 1004_G|A, 1175_A|G, 1367_C|T, 1616_C|T, 1682_C|T, 1739_T|C, 2090_C|T, 2312_C|T, 2366_C|T, 2375_C|T,
2388_T|C, 2435_T|C, 2448_T|C, 2525_G|A, 2561_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2732_G|A, 2925_G|A, 3052_T|C, 3059_G|A, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3254_T|C, 3332_G|A, 3534_G|A,
3615_C|T, 3731_C|T, 3989_T|C, 4013_T|C, 4070_T|C, 4085_T|C, 4130_A|G, 4205_C|T, 4328_C|T, 4382_T|C, 4400_C|T, 4454_G|A, 4478_C|T, 4493_C|T, 4523_G|A, 4607_A|G, 5000_T|C, 5060_T|C, 5066_C|T,
5375_A|G, 5387_C|T, 5390_C|T, 5636_A|G, 5744_A|G, 5828_T|C, 5937_T|C, 6056_C|T, 6152_C|T, 6363_C|T, 6575_A|G, 6581_G|A, 6590_A|G, 6650_A|G, 6684_A|C, 6728_T|C, 6897_C|T, 6926_A|G, 6983_AG|GA,
7050_T|C, 7064_T|C, 7451_A|C, 7496_G|A, 7499_T|C, 7517_C|T, 7580_A|G, 7633_T|C, 7805_T|C, 7967_G|A, 8007_G|A, 8360_A|G, 8408_T|C, 8474_C|T, 8879_T|C, 8882_T|C, 9017_T|C, 9305_C|T, 9353_T|C,
9427_A|G, 9434_A|G, 9440_T|G, 9455_G|A, 9635_G|A, 9722_T|C, 9728_A|G, 9806_C|T, 10070_A|G, 10289_G|A, 10392_A|G, 10477_T|C, 10561_T|C
 Case 3 (A.1): OQ661914.1




Target: 995 samples       Number of changes: 194                                                 


BC: A.1 + A.1             BC BR: 13-14                   BC BR coord: 754 - 755           


Direction L1: <<          Initial region span: 1-6,25-194Gap history (edge excluded): 6-25


Alt. candidates: [], []                                                                                 


Model 1BP/2BP comparison: 1BP vs 2BP: 3.70e-01                                                          


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                             


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 1.050267 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 25 6.813085 None None None * * *



Target sequence

, 254_A|G, 278_G|A, 293_A|G, 423_G|A, 467_T|C, 475_C|T, 523_A|G, 558_T|C, 578_T|C, 653_G|A, 665_C|T, 710_A|G, 719_T|C, 803_A|G, 815_A|G, 896_C|T, 986_C|T, 1055_A|G, 1070_C|T, 1175_A|G,
1292_T|C, 1322_A|G, 1343_C|T, 1398_C|T, 1403_A|G, 1436_T|C, 1457_T|C, 1616_C|T, 1655_C|T, 1694_A|G, 1697_A|G, 1781_C|T, 1842_T|C, 1883_C|T, 1922_C|T, 2030_T|C, 2066_C|T, 2135_C|T, 2285_C|T,
2375_C|T, 2394_A|G, 2411_C|T, 2468_C|T, 2525_G|A, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C, 2768_A|G, 2795_G|A, 2852_G|A, 2864_A|G, 2925_G|A, 2945_C|T, 2978_T|C, 2984_T|C, 3038_T|C,
3052_T|C, 3059_G|A, 3071_A|G, 3083_A|G, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3242_C|T, 3254_T|C, 3279_A|G, 3305_G|A, 3332_G|A, 3338_T|C, 3518_C|T, 3530_G|A, 3534_G|A,
3608_G|A, 3710_T|C, 3718_C|T, 3720_A|G, 3723_T|C, 3731_C|T, 3806_A|T, 3854_A|G, 3885_T|C, 3902_C|T, 3989_T|C, 4085_T|C, 4106_A|G, 4238_C|T, 4295_A|G, 4412_A|G, 4454_G|A, 4481_G|A, 4493_C|T,
4523_G|A, 4592_A|G, 4595_C|T, 4733_T|C, 4751_T|C, 4785_C|T, 4877_C|T, 4901_G|A, 4907_G|A, 4988_G|A, 4995_C|T, 5000_T|C, 5036_C|T, 5060_T|C, 5066_C|T, 5093_T|C, 5369_C|T, 5375_A|G, 5387_C|T,
5414_T|C, 5591_T|C, 5612_T|C, 5657_C|A, 5729_C|T, 5828_T|C, 5900_C|T, 5937_T|C, 6005_C|T, 6056_C|T, 6092_C|T, 6101_T|C, 6164_C|T, 6269_C|T, 6287_T|C, 6363_C|T, 6422_T|C, 6443_G|A, 6473_T|C,
6533_A|G, 6545_C|T, 6566_A|G, 6629_T|C, 6678_T|C, 6684_A|C, 6746_C|T, 6890_A|G, 6983_A|G, 7037_C|T, 7049_CT|TC, 7115_A|G, 7157_C|T, 7451_A|C, 7517_C|T, 7586_T|C, 7633_T|C, 7679_A|G, 7713_T|C,
7775_C|T, 7805_T|C, 7869_C|A, 7961_A|G, 8007_GT|AC, 8105_C|T, 8123_T|C, 8219_G|A, 8342_G|A, 8408_T|C, 8516_A|G, 8606_C|T, 8813_G|A, 8897_A|G, 9017_T|C, 9131_A|G, 9176_C|T, 9209_A|G, 9305_C|T,
9353_T|C, 9434_A|G, 9455_G|A, 9527_A|G, 9623_C|T, 9641_AC|GA, 9677_G|A, 9830_G|A, 9833_C|T, 9882_C|A, 9884_G|A, 9896_T|A, 10151_C|T, 10187_T|C, 10217_A|G, 10281_G|A, 10361_T|C, 10376_G|A,
10392_A|G, 10477_T|C, 10507_A|G, 10509_G|A
 Case 3 (A.1): KU681082.3




Target: 995 samples       Number of changes: 240                                                     


BC: A.1 + A.1             BC BR: 119-120                   BC BR coord: 5287 - 5288           


Direction L1: <<          Initial region span: 1-79,126-240Gap history (edge excluded): 79-126


Alt. candidates: [], []                                                                                     


Model 1BP/2BP comparison: 1BP vs 2BP: 1.93e-10                                                              


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                                 


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 79 3.515692 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 126 11.430201 None None None * * *



Target sequence

, 227_T|C, 254_A|G, 257_T|A, 434_T|C, 455_G|C, 467_T|C, 475_CG|TA, 523_A|G, 558_T|C, 578_T|C, 584_G|A, 639_C|T, 653_G|A, 674_T|C, 689_G|A, 707_C|T, 719_T|C, 803_A|G, 837_T|C, 848_C|T,
895_C|T, 917_C|T, 941_CT|TC, 1070_C|T, 1175_A|G, 1178_C|T, 1214_A|G, 1232_A|G, 1529_A|G, 1587_T|C, 1616_C|T, 1655_C|T, 1670_C|T, 1682_C|T, 1727_C|A, 1814_T|A, 1817_A|C, 1901_T|C, 1904_C|T,
2021_C|T, 2066_C|T, 2084_T|C, 2171_C|T, 2282_A|G, 2285_C|T, 2348_T|C, 2375_C|T, 2394_A|G, 2411_C|T, 2437_T|C, 2483_C|T, 2525_G|A, 2606_C|T, 2648_T|G, 2654_C|T, 2669_T|C, 2681_G|A, 2724_T|C,
2925_G|A, 2969_C|T, 3038_T|C, 3052_T|C, 3059_G|A, 3071_A|G, 3077_T|C, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3195_A|G, 3203_G|A, 3218_T|A, 3254_T|C, 3275_C|T, 3332_G|A, 3365_A|G, 3380_T|C,
3434_G|A, 3461_G|A, 3518_C|T, 3534_G|A, 3575_C|T, 3594_C|T, 3674_T|C, 3731_C|T, 3774_C|T, 3806_A|T, 3854_A|G, 3885_T|C, 3989_T|C, 4085_T|C, 4106_A|G, 4128_T|C, 4146_C|T, 4157_C|T, 4238_C|T,
4295_A|G, 4422_G|A, 4454_G|A, 4481_G|A, 4493_C|T, 4499_C|A, 4523_G|A, 4544_T|C, 4592_A|G, 4595_C|T, 4706_A|T, 4733_T|C, 4751_T|C, 4859_A|G, 4871_T|C, 4957_T|C, 4988_G|A, 5000_T|C, 5060_T|C,
5066_C|T, 5081_C|A, 5193_T|C, 5207_T|C, 5294_T|C, 5336_G|T, 5369_C|T, 5375_A|G, 5387_C|T, 5405_C|T, 5420_T|C, 5429_G|A, 5454_C|T, 5591_T|C, 5624_A|G, 5652_T|A, 5684_A|G, 5693_T|C, 5807_A|G,
5811_C|A, 5828_T|C, 5840_T|C, 5901_C|T, 5975_C|T, 6056_C|T, 6062_C|T, 6065_T|C, 6092_C|T, 6101_T|C, 6128_C|T, 6164_C|T, 6239_T|G, 6246_C|T, 6310_C|T, 6363_C|T, 6443_G|A, 6473_T|C, 6485_G|A,
6684_A|C, 6698_A|G, 6746_C|T, 6797_T|C, 6851_C|T, 6890_A|G, 6944_G|A, 6983_A|G, 6991_T|C, 7037_C|T, 7049_CT|TC, 7064_T|C, 7085_A|G, 7139_A|G, 7208_A|G, 7232_C|T, 7313_T|G, 7415_G|A, 7427_A|G,
7451_A|C, 7517_C|T, 7529_T|C, 7568_T|C, 7633_T|C, 7679_A|G, 7713_T|C, 7793_C|T, 7805_T|C, 7817_G|A, 7853_G|T, 7860_T|C, 7869_C|A, 7871_G|A, 7937_C|T, 7961_A|G, 8007_G|A, 8069_T|C, 8093_G|T,
8105_C|T, 8291_A|G, 8408_T|C, 8516_A|G, 8606_C|T, 8702_C|T, 8813_G|A, 8819_A|G, 8951_C|T, 8993_C|T, 9011_C|T, 9017_T|C, 9119_T|C, 9149_C|T, 9158_C|T, 9176_C|T, 9197_G|A, 9272_C|T, 9305_C|T,
9353_T|C, 9434_A|G, 9455_G|A, 9503_C|T, 9509_T|C, 9518_A|G, 9527_A|G, 9591_T|C, 9617_G|A, 9642_C|A, 9677_G|A, 9818_G|A, 9827_C|T, 9884_G|A, 9893_C|A, 9896_T|A, 10031_C|T, 10109_G|A,
10133_G|A, 10166_G|A, 10199_G|A, 10241_C|T, 10244_C|T, 10262_T|C, 10268_C|T, 10281_G|A, 10334_A|G, 10361_T|C, 10392_A|G, 10561_T|C
 Case 3 (A.1): KX694532.2




Target: 995 samples        Number of changes: 137                                                   


BC: A.1 + A.1.NmC1         BC BR: 131-132                  BC BR coord: 10288 - 10289        


Direction L1: <<           Initial region span: 1-5,134-137Gap history (edge excluded): 5-134


Alt. candidates: [], []                                                                                    


Model 1BP/2BP comparison:  -                                                                               


Rec. model vs L1: 1.49e+09 Rec. model vs L2: 2.12e-262                                              


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 5 0.813045 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 134 1.925944 None None None * * *



Target sequence

, 254_A|G, 398_T|C, 423_G|A, 428_T|C, 467_T|C, 523_A|G, 558_T|C, 653_G|A, 719_T|C, 773_T|C, 803_A|G, 908_T|C, 965_C|T, 974_C|T, 1175_A|G, 1211_T|C, 1328_T|C, 1391_G|A, 1520_G|A, 1616_C|T,
1709_G|A, 1718_C|T, 1763_A|G, 1896_T|C, 1922_C|T, 2066_C|T, 2375_C|T, 2411_C|T, 2519_G|A, 2522_G|A, 2525_G|A, 2537_T|C, 2576_G|A, 2606_C|T, 2648_T|G, 2681_G|A, 2724_T|C, 2846_G|A, 2925_G|A,
3008_A|G, 3014_T|C, 3038_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3266_C|T, 3332_G|A, 3534_G|A, 3731_C|T, 3734_C|T, 3770_T|A, 3870_T|C, 3885_T|C,
3989_T|C, 4076_C|T, 4085_T|C, 4106_A|G, 4238_C|T, 4244_A|G, 4295_A|G, 4403_A|G, 4454_G|A, 4493_C|T, 4523_G|A, 4595_C|T, 4733_T|C, 4886_G|A, 4994_G|A, 5000_T|C, 5060_T|C, 5369_C|T, 5375_A|G,
5387_C|T, 5546_T|C, 5591_T|C, 5744_A|G, 5828_T|C, 5937_T|C, 6008_C|T, 6056_C|T, 6068_A|T, 6101_T|C, 6155_A|G, 6164_C|T, 6275_A|T, 6363_C|T, 6473_T|A, 6684_A|C, 6807_T|C, 6836_A|G, 6851_C|T,
6890_A|G, 6911_C|T, 6935_G|A, 6983_A|G, 7037_C|T, 7043_T|C, 7049_C|T, 7079_A|G, 7136_T|C, 7358_T|C, 7451_A|C, 7517_C|T, 7633_T|C, 7805_T|C, 7847_A|G, 7964_A|G, 8007_G|A, 8105_C|T, 8408_T|C,
8516_A|G, 8606_C|T, 8787_G|A, 9017_T|C, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9491_T|C, 9503_C|T, 9527_A|G, 9821_C|T, 9935_A|G, 10127_T|C, 10163_T|A, 10262_T|C, 10361_T|C, 10376_G|A,
10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): KF993678.1




Target: 995 samples       Number of changes: 132                                                   


BC: A.1 + A.1             BC BR: 122-123                  BC BR coord: 9439 - 9440          


Direction L1: <<          Initial region span: 1-5,124-132Gap history (edge excluded): 5-124


Alt. candidates: [], []                                                                                   


Model 1BP/2BP comparison: 1BP vs 2BP: 2.71e-09                                                            


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                               


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 5 0.813045 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 124 0.9126 None None None * * *



Target sequence

, 254_A|G, 398_T|C, 423_G|A, 428_T|C, 467_T|C, 523_A|G, 558_T|C, 653_G|A, 719_T|C, 773_T|C, 803_A|G, 908_T|C, 965_C|T, 974_C|T, 1175_A|G, 1211_T|C, 1328_T|C, 1391_G|A, 1520_G|A, 1616_C|T,
1709_G|A, 1718_C|T, 1763_A|G, 1896_T|C, 1922_C|T, 2066_C|T, 2375_C|T, 2411_C|T, 2519_G|A, 2522_G|A, 2525_G|A, 2537_T|C, 2576_G|A, 2606_C|T, 2648_T|G, 2681_G|A, 2724_T|C, 2846_G|A, 2925_G|A,
3008_A|G, 3014_T|C, 3038_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3266_C|T, 3332_G|A, 3534_G|A, 3731_C|T, 3734_C|T, 3770_T|A, 3870_T|C, 3885_T|C,
3989_T|C, 4076_C|T, 4085_T|C, 4106_A|G, 4238_C|T, 4244_A|G, 4295_A|G, 4403_A|G, 4454_G|A, 4493_C|T, 4523_G|A, 4595_C|T, 4733_T|C, 4886_G|A, 4994_G|A, 5000_T|C, 5060_T|C, 5369_C|T, 5375_A|G,
5387_C|T, 5546_T|C, 5591_T|C, 5744_A|G, 5828_T|C, 5937_T|C, 6008_C|T, 6056_C|T, 6068_A|T, 6101_T|C, 6155_A|G, 6164_C|T, 6275_A|T, 6363_C|T, 6473_T|A, 6684_A|C, 6807_T|C, 6836_A|G, 6851_C|T,
6890_A|G, 6911_C|T, 6935_G|A, 6983_A|G, 7037_C|T, 7043_T|C, 7049_C|T, 7079_A|G, 7136_T|C, 7358_T|C, 7451_A|C, 7517_C|T, 7633_T|C, 7805_T|C, 7847_A|G, 7964_A|G, 8007_G|A, 8105_C|T, 8408_T|C,
8516_A|G, 8606_C|T, 8787_G|A, 9017_T|C, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9491_T|C, 9503_C|T, 9527_A|G, 9821_C|T, 9935_A|G, 10127_T|C, 10163_T|A, 10262_T|C, 10349_T|C
 Case 3 (A.1): KX051560.1




Target: 995 samples        Number of changes: 129                                                   


BC: A.1 + A.1.NmC1         BC BR: 125-126                  BC BR coord: 10288 - 10289        


Direction L1: <<           Initial region span: 1-4,127-129Gap history (edge excluded): 4-127


Alt. candidates: [], []                                                                                    


Model 1BP/2BP comparison:  -                                                                               


Rec. model vs L1: 3.53e+07 Rec. model vs L2: 0.00e+00                                               


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 4 0.643443 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 127 3.420355 None None None * * *



Target sequence

, 169_T|C, 254_A|G, 423_G|A, 503_CT|TC, 523_A|G, 558_T|C, 578_T|C, 653_G|A, 719_T|C, 764_C|T, 803_A|G, 830_A|T, 842_T|C, 962_T|C, 1175_A|G, 1263_T|C, 1346_G|A, 1424_T|C, 1526_T|C, 1592_T|C,
1616_C|T, 1691_C|T, 1922_C|T, 1985_T|C, 2066_C|T, 2132_T|A, 2210_T|C, 2375_C|T, 2411_C|T, 2525_G|A, 2606_C|T, 2613_T|C, 2648_T|G, 2654_C|T, 2669_T|G, 2681_G|A, 2724_T|C, 2858_C|T, 2915_A|G,
2925_G|A, 2969_C|T, 3038_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3236_G|A, 3254_T|C, 3332_G|A, 3335_C|T, 3518_C|T, 3534_G|A, 3608_G|A, 3731_C|T, 3838_AT|CC, 3954_T|C,
3989_T|C, 4013_T|C, 4085_T|C, 4092_C|T, 4106_A|G, 4140_A|G, 4148_G|A, 4200_T|C, 4422_G|A, 4439_C|T, 4454_G|A, 4523_G|A, 4538_C|T, 4697_T|C, 4733_T|C, 4901_G|A, 5000_T|C, 5060_T|C, 5363_C|T,
5369_C|T, 5375_A|G, 5387_C|T, 5564_C|A, 5591_T|C, 5678_T|C, 5813_T|C, 5828_T|C, 5867_T|C, 5937_T|C, 6056_C|T, 6107_C|T, 6131_G|A, 6363_C|T, 6462_A|C, 6684_A|C, 6908_T|C, 6960_C|T, 6983_A|G,
7037_C|T, 7050_T|C, 7206_A|T, 7451_A|C, 7478_C|T, 7517_C|T, 7592_T|C, 7633_T|C, 7805_T|C, 8007_G|A, 8018_A|G, 8249_C|T, 8372_C|T, 8408_T|C, 8555_C|T, 8570_T|C, 8606_C|T, 8759_G|A, 8780_T|C,
9017_T|C, 9215_C|T, 9296_C|T, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9527_A|G, 9797_T|C, 9950_G|C, 10376_G|A, 10392_A|G, 10477_T|C, 10561_T|C
 Case 3 (A.1): OQ661915.1




Target: 995 samples       Number of changes: 193                                                 


BC: A.1 + A.1             BC BR: 13-14                   BC BR coord: 754 - 755           


Direction L1: <<          Initial region span: 1-6,25-193Gap history (edge excluded): 6-25


Alt. candidates: [], []                                                                                 


Model 1BP/2BP comparison: 1BP vs 2BP: 3.70e-01                                                          


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                             


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 1.050267 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 25 6.643894 None None None * * *



Target sequence

, 254_A|G, 278_G|A, 293_A|G, 423_G|A, 467_T|C, 475_C|T, 523_A|G, 558_T|C, 578_T|C, 653_G|A, 665_C|T, 710_A|G, 719_T|C, 803_A|G, 815_A|G, 896_C|T, 986_C|T, 1055_A|G, 1070_C|T, 1175_A|G,
1292_T|C, 1322_A|G, 1343_C|T, 1398_C|T, 1403_A|G, 1436_T|C, 1457_T|C, 1616_C|T, 1655_C|T, 1694_A|G, 1697_A|G, 1781_C|T, 1842_T|C, 1883_C|T, 1922_C|T, 2030_T|C, 2066_C|T, 2135_C|T, 2285_C|T,
2375_C|T, 2394_A|G, 2411_C|T, 2468_C|T, 2525_G|A, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C, 2768_A|G, 2795_G|A, 2852_G|A, 2864_A|G, 2925_G|A, 2945_C|T, 2984_T|C, 3038_T|C, 3052_T|C,
3059_G|A, 3071_A|G, 3083_A|G, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3242_C|T, 3254_T|C, 3279_A|G, 3305_G|A, 3332_G|A, 3338_T|C, 3518_C|T, 3530_G|A, 3534_G|A, 3608_G|A,
3710_T|C, 3718_C|T, 3720_A|G, 3723_T|C, 3731_C|T, 3806_A|T, 3854_A|G, 3885_T|C, 3902_C|T, 3989_T|C, 4085_T|C, 4106_A|G, 4238_C|T, 4295_A|G, 4412_A|G, 4454_G|A, 4481_G|A, 4493_C|T, 4523_G|A,
4592_A|G, 4595_C|T, 4733_T|C, 4751_T|C, 4785_C|T, 4877_C|T, 4901_G|A, 4907_G|A, 4988_G|A, 4995_C|T, 5000_T|C, 5036_C|T, 5060_T|C, 5066_C|T, 5093_T|C, 5369_C|T, 5375_A|G, 5387_C|T, 5414_T|C,
5591_T|C, 5612_T|C, 5657_C|A, 5729_C|T, 5828_T|C, 5900_C|T, 5937_T|C, 6005_C|T, 6056_C|T, 6092_C|T, 6101_T|C, 6164_C|T, 6269_C|T, 6287_T|C, 6363_C|T, 6422_T|C, 6443_G|A, 6473_T|C, 6533_A|G,
6545_C|T, 6566_A|G, 6629_T|C, 6678_T|C, 6684_A|C, 6746_C|T, 6890_A|G, 6983_A|G, 7037_C|T, 7049_CT|TC, 7115_A|G, 7157_C|T, 7451_A|C, 7517_C|T, 7586_T|C, 7633_T|C, 7679_A|G, 7713_T|C, 7775_C|T,
7805_T|C, 7869_C|A, 7961_A|G, 8007_GT|AC, 8105_C|T, 8123_T|C, 8219_G|A, 8342_G|A, 8408_T|C, 8516_A|G, 8606_C|T, 8813_G|A, 8897_A|G, 9017_T|C, 9131_A|G, 9176_C|T, 9209_A|G, 9305_C|T, 9353_T|C,
9434_A|G, 9455_G|A, 9527_A|G, 9623_C|T, 9641_AC|GA, 9677_G|A, 9830_G|A, 9833_C|T, 9882_C|A, 9884_G|A, 9896_T|A, 10151_C|T, 10187_T|C, 10217_A|G, 10281_G|A, 10361_T|C, 10376_G|A, 10392_A|G,
10477_T|C, 10507_A|G, 10509_G|A
 Case 3 (A.1): KX051561.1




Target: 995 samples        Number of changes: 137                                                   


BC: A.1 + A.1.NmC1         BC BR: 131-132                  BC BR coord: 10288 - 10289        


Direction L1: <<           Initial region span: 1-3,134-137Gap history (edge excluded): 3-134


Alt. candidates: [], []                                                                                    


Model 1BP/2BP comparison:  -                                                                               


Rec. model vs L1: 9.41e+13 Rec. model vs L2: 3.67e-261                                              


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 3 0.386836 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 134 1.925944 NaN NaN NaN * * *
A.1 995 123 0.758465 -1.268593 16.537187 1.328857e+08 *



Target sequence

, 254_A|G, 423_G|A, 467_T|C, 523_A|G, 558_T|C, 575_T|C, 653_G|A, 719_T|C, 749_A|G, 803_A|G, 810_T|C, 884_A|G, 1175_A|G, 1325_C|T, 1616_C|T, 1718_C|T, 1896_T|C, 1922_C|T, 2060_T|A, 2066_C|T,
2207_A|G, 2375_C|T, 2411_C|T, 2519_G|A, 2525_G|A, 2576_G|A, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A, 2717_C|T, 2724_T|C, 2804_C|T, 2846_G|A, 2873_G|A, 2925_G|A, 2973_G|A, 3038_T|C, 3059_G|A,
3110_T|C, 3131_G|A, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3266_C|T, 3332_G|A, 3518_C|T, 3534_G|A, 3720_A|G, 3731_C|T, 3885_T|C, 3989_T|C, 4085_T|C, 4106_A|G, 4238_C|T, 4287_G|A,
4295_A|G, 4454_G|A, 4481_G|A, 4493_C|T, 4523_G|A, 4595_C|T, 4652_A|G, 4688_A|G, 4733_T|C, 4850_C|T, 4916_C|T, 4952_C|T, 5000_T|C, 5060_T|C, 5189_A|G, 5198_T|C, 5369_C|T, 5375_A|G, 5387_C|T,
5450_T|C, 5546_T|C, 5585_C|T, 5591_T|C, 5744_A|G, 5828_T|C, 5937_T|C, 6056_C|T, 6101_T|C, 6155_A|G, 6164_C|T, 6275_A|T, 6363_C|T, 6473_T|A, 6684_A|C, 6755_C|T, 6807_T|C, 6890_A|G, 6911_C|T,
6983_A|G, 6989_C|T, 7037_C|T, 7050_T|C, 7064_T|C, 7079_A|G, 7358_T|C, 7451_A|C, 7517_C|T, 7633_T|C, 7766_C|T, 7769_G|A, 7805_T|C, 8007_G|A, 8105_C|T, 8351_C|T, 8408_T|C, 8516_A|G, 8606_C|T,
8651_C|T, 9017_T|C, 9098_T|C, 9137_T|C, 9305_C|T, 9353_T|C, 9434_A|G, 9503_C|T, 9509_T|C, 9527_A|G, 9582_C|T, 9591_T|C, 9623_C|T, 9992_A|G, 10071_A|C, 10161_G|A, 10376_G|A, 10382_A|G,
10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): PP115590.1




Target: 995 samples        Number of changes: 114                                                   


BC: A.1 + A.1.NmC1         BC BR: 108-109                  BC BR coord: 10288 - 10289        


Direction L1: >>           Initial region span: 1-3,110-114Gap history (edge excluded): 3-110


Alt. candidates: [], []                                                                                    


Model 1BP/2BP comparison:  -                                                                               


Rec. model vs L1: 6.29e+12 Rec. model vs L2: 5.07e-297                                              


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 3 0.120431 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 110 4.261319 None None None * * *



Target sequence

, 254_A|G, 326_G|A, 423_G|A, 558_T|C, 653_G|A, 746_T|C, 803_A|G, 998_C|T, 1175_A|G, 1598_T|C, 1616_C|T, 1656_G|A, 2079_A|G, 2287_C|T, 2291_C|T, 2375_C|T, 2411_C|T, 2486_T|C, 2525_G|A,
2606_C|T, 2623_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 2975_A|T, 3018_T|C, 3038_T|C, 3059_G|A, 3110_T|C, 3127_A|G, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3254_T|C, 3332_G|A, 3518_C|T,
3534_G|A, 3572_C|T, 3704_C|T, 3731_C|T, 3740_C|T, 3783_A|G, 3989_T|C, 3992_C|T, 4085_T|C, 4106_A|G, 4424_C|T, 4454_G|A, 4523_G|A, 4601_G|A, 4766_C|T, 5000_T|C, 5003_C|T, 5060_T|C, 5084_A|G,
5099_T|C, 5258_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5543_G|A, 5591_T|C, 5678_T|C, 5702_T|C, 5828_T|C, 5937_T|C, 6056_C|T, 6310_C|T, 6518_A|G, 6684_A|C, 6785_T|C, 6848_T|C, 6983_A|G, 7028_A|G,
7031_T|C, 7050_T|C, 7250_C|T, 7397_A|T, 7451_A|C, 7496_G|A, 7517_C|T, 7586_T|C, 7633_T|C, 7805_T|C, 7835_C|T, 8007_G|A, 8208_A|G, 8408_T|C, 8606_C|T, 8753_T|C, 8933_T|C, 8950_A|G, 9017_T|C,
9146_G|A, 9149_C|T, 9305_C|T, 9324_C|T, 9353_T|C, 9362_G|A, 9434_A|G, 9455_G|A, 9800_C|T, 9890_C|T, 9941_A|G, 10010_T|C, 10188_T|C, 10376_G|A, 10392_A|G, 10460_A|G, 10477_T|C, 10561_T|C,
10744_C|T
 Case 3 (A.1): KU681081.3




Target: 995 samples        Number of changes: 110                                                   


BC: A.1 + A.1.NmC1         BC BR: 105-106                  BC BR coord: 10288 - 10289        


Direction L1: <<           Initial region span: 1-3,107-110Gap history (edge excluded): 3-107


Alt. candidates: [], []                                                                                    


Model 1BP/2BP comparison:  -                                                                               


Rec. model vs L1: 1.29e+07 Rec. model vs L2: 5.31e-278                                              


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 3 0.120431 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 107 4.261319 None None None * * *



Target sequence

, 254_A|G, 326_G|A, 423_G|A, 523_A|G, 558_T|C, 653_G|A, 746_T|C, 803_A|G, 998_C|T, 1175_A|G, 1598_T|C, 1616_C|T, 1656_G|A, 2079_A|G, 2287_C|T, 2291_C|T, 2375_C|T, 2411_C|T, 2486_T|C,
2525_G|A, 2606_C|T, 2623_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3018_T|C, 3038_T|C, 3059_G|A, 3110_T|C, 3127_A|G, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3254_T|C, 3332_G|A, 3518_C|T,
3534_G|A, 3572_C|T, 3704_C|T, 3731_C|T, 3740_C|T, 3783_A|G, 3989_T|C, 3992_C|T, 4085_T|C, 4106_A|G, 4424_C|T, 4454_G|A, 4523_G|A, 4601_G|A, 4766_C|T, 5000_T|C, 5003_C|T, 5060_T|C, 5084_A|G,
5099_T|C, 5258_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5543_G|A, 5591_T|C, 5702_T|C, 5828_T|C, 5937_T|C, 6056_C|T, 6310_C|T, 6518_A|G, 6684_A|C, 6785_T|C, 6848_T|C, 6983_A|G, 7028_A|G, 7031_T|C,
7050_T|C, 7250_C|T, 7397_A|T, 7451_A|C, 7496_G|A, 7517_C|T, 7586_T|C, 7633_T|C, 7805_T|C, 8007_G|A, 8208_A|G, 8408_T|C, 8606_C|T, 8753_T|C, 8933_T|C, 9017_T|C, 9146_G|A, 9149_C|T, 9305_C|T,
9324_C|T, 9353_T|C, 9362_G|A, 9434_A|G, 9455_G|A, 9800_C|T, 9890_C|T, 9941_A|G, 10010_T|C, 10188_T|C, 10376_G|A, 10392_A|G, 10460_A|G, 10477_T|C, 10561_T|C
 Case 3 (A.1): KX051562.1




Target: 995 samples        Number of changes: 144                                                   


BC: A.1 + A.1.NmC1         BC BR: 137-138                  BC BR coord: 10288 - 10289        


Direction L1: <<           Initial region span: 1-4,141-144Gap history (edge excluded): 4-141


Alt. candidates: [], []                                                                                    


Model 1BP/2BP comparison:  -                                                                               


Rec. model vs L1: 4.28e+12 Rec. model vs L2: 1.19e-104                                              


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 4 0.523685 NaN NaN NaN * * *
A.1.NmC2 83 3 -9.920764 -1101.399642 2500.799283 0.0 *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 141 1.925944 None None None * * *



Target sequence

, 50_A|G, 56_G|A, 254_A|G, 423_G|A, 455_G|A, 467_T|C, 479_G|A, 523_A|G, 558_T|C, 803_A|G, 884_A|G, 974_C|T, 1115_T|C, 1175_A|G, 1211_T|C, 1370_G|A, 1616_C|T, 1718_C|T, 1745_G|A, 1896_T|C,
1902_A|G, 2060_T|A, 2066_C|T, 2207_A|G, 2225_A|G, 2333_T|C, 2375_C|T, 2411_C|T, 2519_G|A, 2525_G|A, 2555_T|C, 2576_G|A, 2606_C|T, 2648_T|G, 2654_C|T, 2724_T|C, 2726_G|A, 2756_T|A, 2819_G|A,
2846_G|A, 2925_G|A, 3014_T|C, 3038_T|C, 3041_T|A, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3266_C|T, 3332_G|A, 3518_C|T, 3534_G|A, 3641_C|T, 3731_C|T,
3885_T|C, 3989_T|C, 3992_C|T, 4085_T|C, 4106_A|G, 4238_C|T, 4286_C|T, 4295_A|G, 4454_G|A, 4493_C|T, 4523_G|A, 4595_C|T, 4652_A|G, 4733_T|C, 4790_A|G, 4850_C|T, 4952_C|T, 5000_T|C, 5060_T|C,
5177_G|A, 5198_T|C, 5267_T|C, 5279_A|G, 5324_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5546_T|C, 5591_T|C, 5612_T|C, 5744_A|G, 5828_T|C, 5937_T|C, 6056_C|T, 6101_T|C, 6155_A|G, 6164_C|T, 6275_A|T,
6470_G|A, 6473_T|A, 6684_A|C, 6807_T|C, 6890_A|G, 6911_C|T, 6983_A|G, 7037_C|T, 7050_T|C, 7079_A|G, 7451_A|C, 7517_C|T, 7574_C|T, 7633_T|C, 7713_T|C, 7784_G|A, 7805_T|C, 7887_T|C, 7931_T|C,
8007_G|A, 8105_C|T, 8408_T|C, 8516_A|G, 8606_C|T, 8630_AA|GG, 8696_C|T, 8991_C|T, 9017_T|C, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9503_C|T, 9509_T|C, 9527_A|G, 9558_C|T, 9560_A|G, 9591_T|C,
9695_T|C, 9767_T|A, 9809_C|T, 10310_G|A, 10337_T|G, 10376_G|A, 10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): KY558996.1




Target: 995 samples       Number of changes: 32                                                             


BC: A.1 + A.1.NmC2 + A.1  BC BR: 7-8, 9-10                  BC BR coord: 1397 - 1398, 1990 - 1991    


Direction L1: <<          Initial region span: 1-7,8-9,26-32Gap history (edge excluded): 7-26 -> 9-26


Alt. candidates: [], []                                                                                            


Model 1BP/2BP comparison: 2BP vs 1BP: 5.07e-01                                                                     


Rec. model vs L1: 6.86e-02Rec. model vs L2: 2.35e-58                                                        


Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 7 0.145129 None None None * * *
|||||

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 9 2.473360 NaN NaN NaN * * *
A.1 995 10 -0.970950 -1.206281 8.412562 0.025223 * *
A.1.NmC1 181 8 -1.160516 -2.987031 11.974061 0.004254 * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 26 0.356493 None None None * * *



Target sequence

, 254_A|G, 428_T|A, 616_C|T, 1232_A|G, 1298_T|C, 1364_C|T, 1387_A|T, 1398_C|T, 1616_C|T, 2330_A|G, 2375_C|T, 2534_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A,
3332_G|A, 3534_G|A, 3731_C|T, 3989_T|C, 5937_T|C, 6983_A|G, 7370_A|T, 7451_A|C, 7633_T|C, 7805_T|C, 8420_G|A, 9305_C|T, 9353_T|C
 Case 3 (A.1): MF352141.1




Target: 995 samples       Number of changes: 33                                                 


BC: A.1 + A.1             BC BR: 17-18                  BC BR coord: 3898 - 3899         


Direction L1: <<          Initial region span: 1-3,18-33Gap history (edge excluded): 3-18


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 2.67e-07                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 3 0.725053 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 18 1.575835 None None None * * *



Target sequence

, 419_A|G, 1044_G|A, 1313_C|T, 1616_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2853_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3459_C|T, 3534_G|A, 3731_C|T, 3987_G|A, 4193_A|G,
5676_C|T, 5937_T|C, 6983_A|G, 6992_A|G, 7229_A|G, 7442_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 8777_C|T, 9305_C|T, 9353_T|C, 9557_T|C, 10561_T|C
 Case 3 (A.1): OQ727568.1




Target: 995 samples       Number of changes: 33                                                 


BC: A.1 + A.1             BC BR: 10-11                  BC BR coord: 3136 - 3137         


Direction L1: <<          Initial region span: 1-4,17-33Gap history (edge excluded): 4-17


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 1.30e-09                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 4 0.350456 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 17 1.440617 None None None * * *



Target sequence

, 254_A|G, 479_G|A, 1044_G|A, 1313_C|T, 1616_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3254_T|C, 3332_G|A, 3534_G|A, 3692_T|C, 3731_C|T, 5676_C|T,
5921_T|C, 5937_T|C, 6224_A|G, 6308_C|T, 6606_T|C, 6930_T|C, 6957_C|T, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9305_C|T, 9353_T|C, 10561_T|C
 Case 3 (A.1): KU707826.1




Target: 995 samples       Number of changes: 37                                                   


BC: A.1 + A.1             BC BR: 31-32                   BC BR coord: 9295 - 9296          


Direction L1: >>          Initial region span: 1-31,35-37Gap history (edge excluded): 31-35


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 2.03e-05                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 31 2.070487 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 35 0.470661 None None None * * *



Target sequence

, 80, 254_A|G, 1034_T|C, 1433_C|T, 1475_G|A, 1616_C|T, 1904_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3566_T|C, 3731_C|T,
5315_A|G, 5937_T|C, 6671_T|C, 6803_C|T, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 8213_A|G, 8327_C|T, 8978_C|T, 9242_C|T, 9305_C|T, 9344_G|A, 9353_T|C, 10181_T|C, 10386_A|G, 10561_T|C
 Case 3 (A.1): KU497555.1




Target: 995 samples       Number of changes: 43                                                 


BC: A.1 + A.1             BC BR: 18-19                  BC BR coord: 3253 - 3254         


Direction L1: <<          Initial region span: 1-7,33-43Gap history (edge excluded): 7-33


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 4.75e-07                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 7 1.129671 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 33 1.481064 None None None * * *



Target sequence

, 254_A|G, 398_T|C, 443_T|C, 1061_A|G, 1533_C|T, 1616_C|T, 1756_G|C, 2375_C|T, 2534_C|T, 2603_C|T, 2681_G|A, 2714_C|T, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A,
3534_G|A, 3731_C|T, 3882_C|T, 3989_T|C, 4472_T|C, 5081_C|A, 5495_T|C, 5937_T|C, 6026_T|C, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 8207_T|C, 8558_G|A, 8599_A|T, 8840_G|A, 9305_C|T, 9353_T|C,
10268_C|T, 10378_A|G, 10451_C|T, 10467_A|T, 10561_T|C
 Case 3 (A.1): KX446950.2




Target: 995 samples       Number of changes: 45                                                 


BC: A.1 + A.1             BC BR: 5-6                    BC BR coord: 1990 - 1991         


Direction L1: <<          Initial region span: 1-4,10-45Gap history (edge excluded): 4-10


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 2.89e-03                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 4 0.452528 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 10 3.690812 None None None * * *



Target sequence

, 254_A|G, 637_T|C, 968_G|A, 1115_T|C, 1616_C|T, 2192_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 2978_T|C, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3282_A|G, 3332_G|A, 3534_G|A,
3617_G|A, 3731_C|T, 3863_G|A, 4607_A|G, 4731_G|A, 4784_G|A, 5087_T|C, 5195_G|A, 5315_A|G, 5937_T|C, 6327_A|C, 6725_T|C, 6737_C|T, 6983_A|G, 7223_A|G, 7307_T|C, 7451_A|C, 7633_T|C, 7667_T|C,
7805_T|C, 8480_A|G, 9240_C|T, 9246_C|T, 9305_C|T, 9353_T|C, 10561_T|C
 Case 3 (A.1): KY559032.1




Target: 995 samples       Number of changes: 29                                                 


BC: A.1 + A.1             BC BR: 6-7                    BC BR coord: 2653 - 2654         


Direction L1: <<          Initial region span: 1-6,18-29Gap history (edge excluded): 6-18


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 1.98e-03                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 0.492341 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 18 0.958487 None None None * * *



Target sequence

, 254_A|G, 467_T|C, 1616_C|T, 1853_C|T, 2375_C|T, 2613_T|C, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3731_C|T, 3821_T|C, 4784_G|A, 5937_T|C,
6223_A|G, 6851_C|T, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 8798_G|A, 8950_A|G, 9305_C|T, 9353_T|C
 Case 3 (A.1): KY648934.1




Target: 995 samples       Number of changes: 46                                                 


BC: A.1 + A.1             BC BR: 9-10                   BC BR coord: 3031 - 3032         


Direction L1: <<          Initial region span: 1-9,17-46Gap history (edge excluded): 9-17


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 3.82e-02                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 9 0.226118 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 17 3.881601 None None None * * *



Target sequence

, 254_A|G, 1115_T|C, 1616_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 2978_T|C, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3223_A|C, 3332_G|A, 3534_G|A, 3617_G|A, 3731_C|T, 3818_A|G,
3863_G|A, 3895_C|T, 4226_C|T, 4607_A|G, 4731_G|A, 4784_G|A, 5087_T|C, 5195_G|A, 5315_A|G, 5450_T|C, 5937_T|C, 6327_A|C, 6377_A|G, 6629_T|C, 6725_T|C, 6737_C|T, 6983_A|G, 7307_T|C, 7451_A|C,
7633_T|C, 7805_T|C, 9240_C|T, 9305_C|T, 9353_T|C, 9476_C|T, 9591_T|C, 10561_T|C
 Case 3 (A.1): MN473454.1




Target: 995 samples        Number of changes: 55                                                 


BC: A.1.NmC2 + A.1         BC BR: 6-7                    BC BR coord: 1405 - 1406         


Direction L1: <<           Initial region span: 1-4,31-55Gap history (edge excluded): 4-31


Alt. candidates: [], []                                                                                 


Model 1BP/2BP comparison:  -                                                                            


Rec. model vs L1: 2.60e-146Rec. model vs L2: 1.92e+12                                            


Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 4 -9.496088 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 31 1.620716 None None None * * *



Target sequence

, 227_T|C, 254_A|G, 875_C|T, 881_G|T, 923_G|A, 1398_C|T, 1472_G|A, 1616_C|T, 1904_C|T, 2375_C|T, 2534_C|T, 2600_C|T, 2681_G|A, 2724_T|C, 2882_C|T, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A,
3218_T|A, 3323_G|A, 3332_G|A, 3534_G|A, 3566_T|C, 3593_T|C, 3731_C|T, 3767_A|G, 3788_G|A, 3879_T|A, 3911_A|G, 4175_C|T, 4709_T|C, 5315_A|G, 5879_T|C, 5937_T|C, 6053_T|A, 6629_T|A, 6671_T|C,
6983_A|G, 7073_C|T, 7094_T|C, 7451_A|C, 7633_T|C, 7678_C|T, 7805_T|C, 8225_A|G, 8594_C|T, 8702_C|T, 9137_T|C, 9296_C|T, 9305_C|T, 9353_T|C, 9365_A|T, 9854_C|T, 10561_T|C
 Case 3 (A.1): PP470595.1




Target: 995 samples          Number of changes: 39                                                             


BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 5-6, 34-35                 BC BR coord: 901 - 902, 7516 - 7517      


Direction L1: >>             Initial region span: 1-5,6-7,37-39Gap history (edge excluded): 5-37 -> 7-37


Alt. candidates: [], []                                                                                               


Model 1BP/2BP comparison:    2BP vs 1BP: 1.98e-22                                                                     


Rec. model vs L1: 3.45e-38   Rec. model vs L2: 7.34e-07                                                        


Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 5 9.392444 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 7 0.410036 NaN NaN NaN * * *
A.1.NmC2 83 6 -0.113981 -53.319458 234.638916 1.977576e-22 *
A.1.NmC1 181 6 -10.000000 -157.438820 442.877639 1.195066e-67 *
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 37 2.251673 None None None * * *



Target sequence

, 254_A|G, 428_T|A, 755_T|C, 875_C|T, 881_G|T, 902_T|G, 1394_A|C, 1398_C|T, 1616_C|T, 2006_T|C, 2279_T|C, 2375_C|T, 2534_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A,
3218_T|A, 3279_A|G, 3332_G|A, 3459_C|T, 3534_G|A, 3731_C|T, 3902_C|T, 3989_T|C, 4448_T|C, 4709_T|C, 5937_T|C, 6008_C|T, 6983_A|G, 7196_G|A, 7451_A|C, 7633_T|C, 7805_T|C, 9305_C|T, 9353_T|C,
10164_A|G
 Case 3 (A.1): PP626401.1




Target: 995 samples       Number of changes: 163                                                 


BC: A.1 + A.1             BC BR: 28-29                   BC BR coord: 1990 - 1991         


Direction L1: <<          Initial region span: 1-6,98-163Gap history (edge excluded): 6-98


Alt. candidates: [], []                                                                                 


Model 1BP/2BP comparison: 1BP vs 2BP: 1.78e-01                                                          


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                             


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 0.914843 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 98 2.393317 None None None * * *



Target sequence

, 47_C|T, 254_A|G, 423_G|A, 428_T|C, 467_T|C, 476_G|A, 523_A|G, 558_T|C, 653_G|A, 719_T|C, 773_T|C, 803_A|G, 884_A|G, 974_C|T, 1046_T|C, 1175_A|G, 1328_T|C, 1391_G|A, 1520_G|A, 1526_T|C,
1592_T|C, 1616_C|T, 1718_C|T, 1748_T|C, 1763_A|G, 1875_T|C, 1896_T|C, 1922_C|T, 2057_C|T, 2066_C|T, 2148_G|A, 2375_C|T, 2411_C|T, 2436_A|G, 2471_A|G, 2519_G|A, 2522_G|A, 2525_G|A, 2567_A|G,
2576_G|A, 2606_C|T, 2648_T|G, 2681_G|A, 2724_T|C, 2846_G|A, 2925_G|A, 2951_T|C, 2969_C|T, 3008_A|G, 3014_T|C, 3038_T|C, 3059_G|A, 3089_C|T, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A,
3218_T|A, 3254_T|C, 3266_C|T, 3332_G|A, 3534_G|A, 3665_G|A, 3731_C|T, 3869_CT|TC, 3885_T|C, 3977_T|C, 3989_T|C, 3992_C|T, 4010_G|A, 4031_C|T, 4085_T|C, 4106_A|G, 4238_C|T, 4244_A|G, 4295_A|G,
4403_A|G, 4445_C|T, 4454_G|T, 4493_C|T, 4523_G|A, 4562_C|T, 4595_C|T, 4733_T|C, 4943_G|A, 4961_T|C, 5000_T|C, 5003_C|T, 5060_T|C, 5210_G|A, 5369_C|T, 5375_A|G, 5387_C|T, 5546_T|C, 5591_T|C,
5744_A|G, 5828_T|C, 5867_T|C, 5937_T|C, 6101_T|C, 6119_C|T, 6155_A|G, 6164_C|T, 6230_A|G, 6233_T|C, 6275_A|T, 6278_C|T, 6473_T|A, 6645_C|T, 6684_A|C, 6807_T|C, 6851_C|T, 6890_A|G, 6911_C|T,
6935_G|A, 6938_A|G, 6983_A|G, 7037_C|T, 7043_T|C, 7049_CT|TC, 7079_A|G, 7151_T|C, 7358_T|C, 7451_A|C, 7517_C|T, 7633_T|C, 7805_T|C, 7811_G|A, 7886_C|T, 7964_A|G, 8007_G|A, 8105_C|T, 8408_T|C,
8516_A|G, 8606_C|T, 8787_G|A, 8852_T|C, 9017_T|C, 9110_G|A, 9206_A|G, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9503_C|T, 9527_A|G, 9557_T|C, 9671_T|A, 9797_T|C, 9881_C|T, 9935_A|G, 10052_T|C,
10127_T|C, 10165_C|T, 10275_A|C, 10361_T|C, 10376_G|A, 10392_A|G, 10477_T|C, 10513_C|T, 10561_T|C, 10613_C|T
 Case 3 (A.1): MT636065.1




Target: 995 samples        Number of changes: 47                                                   


BC: A.1 + A.1.NmC1         BC BR: 44-45                   BC BR coord: 10391 - 10392        


Direction L1: >>           Initial region span: 1-31,45-47Gap history (edge excluded): 31-45


Alt. candidates: [], []                                                                                   


Model 1BP/2BP comparison:  -                                                                              


Rec. model vs L1: 5.21e+00 Rec. model vs L2: 4.30e-183                                             


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 31 2.574448 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 45 1.972602 None None None * * *



Target sequence

, 254_A|G, 467_T|C, 737_A|T, 1263_T|C, 1547_T|C, 1616_C|T, 1931_G|T, 2178_C|T, 2375_C|T, 2474_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3260_A|G, 3279_A|G,
3332_G|A, 3534_G|A, 3712_A|G, 3731_C|T, 3918_C|T, 4152_C|T, 4287_G|A, 4607_A|G, 4757_T|C, 5937_T|C, 6353_G|A, 6596_G|A, 6734_C|T, 6983_A|G, 7211_T|C, 7451_A|C, 7633_T|C, 7805_T|C, 8186_A|G,
8714_G|A, 8879_T|G, 9305_C|T, 9353_T|C, 9383_C|T, 9581_G|A, 10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): KY317937.1




Target: 995 samples          Number of changes: 41                                                                  


BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 21-22, 38-39                  BC BR coord: 3898 - 3899, 9304 - 9305      


Direction L1: >>             Initial region span: 1-21,31-38,39-41Gap history (edge excluded): 21-39 -> 21-31


Alt. candidates: [], []                                                                                                    


Model 1BP/2BP comparison:    2BP vs 1BP: 1.47e-36                                                                          


Rec. model vs L1: 6.62e-56   Rec. model vs L2: 4.06e-12                                                             


Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 21 17.0895 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 31 1.060445 NaN NaN NaN * * *
A.1.NmC1 181 39 0.000000 -132.580922 353.161843 2.304665e-58
A.1.NmC2 83 39 -1.529105 -82.378496 252.756993 1.459455e-36
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 39 2.251673 None None None * * *



Target sequence

, 254_A|G, 428_T|A, 755_T|C, 875_C|T, 881_G|T, 902_T|G, 1398_C|T, 1616_C|T, 2375_C|T, 2534_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3459_C|T,
3534_G|A, 3731_C|T, 3902_C|T, 3989_T|C, 4448_T|C, 4886_G|A, 5240_C|T, 5540_G|A, 5937_T|C, 6008_C|T, 6983_A|G, 7208_A|G, 7451_A|C, 7633_T|C, 7712_C|T, 7787_C|T, 7805_T|C, 8555_C|T, 8832_C|T,
9305_C|T, 9353_T|C, 10164_A|G
 Case 3 (A.1): PQ129534.1




Target: 995 samples       Number of changes: 43                                                 


BC: A.1 + A.1             BC BR: 5-6                    BC BR coord: 1990 - 1991         


Direction L1: <<          Initial region span: 1-4,10-43Gap history (edge excluded): 4-10


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 2.89e-03                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 4 0.452528 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 10 3.910219 None None None * * *



Target sequence

, 254_A|G, 637_T|C, 968_G|A, 1115_T|C, 1616_C|T, 2192_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 2978_T|C, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3617_G|A,
3731_C|T, 3863_G|A, 4607_A|G, 4731_G|A, 4784_G|A, 5087_T|C, 5195_G|A, 5315_A|G, 5937_T|C, 6327_A|C, 6725_T|C, 6737_C|T, 6983_A|G, 7223_A|G, 7307_T|C, 7451_A|C, 7633_T|C, 7667_T|C, 7805_T|C,
8480_A|G, 9240_C|T, 9246_C|T, 9305_C|T, 9353_T|C
 Case 3 (A.1): OK054444.1




Target: 995 samples       Number of changes: 51                                               


BC: A.1 + A.1             BC BR: 8-9                   BC BR coord: 2404 - 2405        


Direction L1: <<          Initial region span: 1-6,9-51Gap history (edge excluded): 6-9


Alt. candidates: [], []                                                                              


Model 1BP/2BP comparison: 1BP vs 2BP: 4.38e-05                                                       


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                          


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 0.760176 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 9 5.200961 None None None * * *



Target sequence

, 254_A|G, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3517_G|A,
3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4373_C|T, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6350_G|A, 6725_T|C, 6737_C|T, 6755_C|T,
6938_A|G, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 9410_C|T, 10052_T|C, 10561_T|C
 Case 3 (A.1): KY272991.1




Target: 995 samples       Number of changes: 39                                                   


BC: A.1 + A.1             BC BR: 27-28                   BC BR coord: 6505 - 6506          


Direction L1: >>          Initial region span: 1-27,33-39Gap history (edge excluded): 27-33


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 8.44e-05                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 27 0.947804 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 33 0.504092 None None None * * *



Target sequence

, 254_A|G, 1139_G|A, 1400_G|A, 1616_C|T, 2375_C|T, 2624_A|T, 2681_G|A, 2724_T|C, 2773_A|G, 2879_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3344_C|T, 3534_G|A, 3731_C|T,
3936_G|A, 4397_C|T, 4784_G|A, 4883_C|T, 5315_A|G, 5937_T|C, 6223_A|G, 6437_A|G, 6983_A|G, 7304_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 7877_C|T, 9305_C|T, 9353_T|C, 9533_T|C, 9905_G|A, 10561_T|C,
10694_A|G
 Case 3 (A.1): MF801385.1




Target: 995 samples       Number of changes: 40                                               


BC: A.1 + A.1             BC BR: 7-8                   BC BR coord: 2731 - 2732        


Direction L1: <<          Initial region span: 1-4,8-40Gap history (edge excluded): 4-8


Alt. candidates: [], []                                                                              


Model 1BP/2BP comparison: 1BP vs 2BP: 2.36e-06                                                       


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                          


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 4 0.274353 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 8 4.353871 None None None * * *



Target sequence

, 1616_C|T, 1904_C|T, 2375_C|T, 2555_T|C, 2654_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3996_A|T,
4440_C|T, 4697_T|C, 4784_G|A, 5195_G|A, 5315_A|G, 5588_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6725_T|C, 6737_C|T, 6755_C|T, 7451_A|C, 8454_A|T, 8872_A|G, 9240_C|T, 9305_C|T, 9353_T|C, 9767_T|A,
10561_T|C, 10696_A|G
 Case 3 (A.1): KY559027.1




Target: 995 samples       Number of changes: 34                                                 


BC: A.1 + A.1             BC BR: 4-5                    BC BR coord: 2404 - 2405         


Direction L1: <<          Initial region span: 1-3,27-34Gap history (edge excluded): 3-27


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 1.19e-07                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 3 0.18835 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 27 0.858819 None None None * * *



Target sequence

, 254_A|G, 1616_C|T, 2222_G|A, 2375_C|T, 2442_T|C, 2534_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3002_T|C, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3731_C|T, 3945_T|C, 3989_T|C,
4874_C|T, 5267_T|C, 5937_T|C, 6716_A|G, 6983_A|G, 7058_T|C, 7451_A|C, 7505_C|T, 7633_T|C, 7805_T|C, 8057_G|A, 9305_C|T, 9353_T|C, 10052_T|C, 10253_T|C
 Case 3 (A.1): KX013000.1




Target: 995 samples       Number of changes: 54                                                   


BC: A.1 + A.1             BC BR: 48-49                   BC BR coord: 9439 - 9440          


Direction L1: >>          Initial region span: 1-37,49-54Gap history (edge excluded): 37-49


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 2.95e-05                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 37 1.883755 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 49 0.088061 None None None * * *



Target sequence

, 254_A|G, 266_T|C, 433_G|A, 806_C|T, 1175_A|G, 1616_C|T, 2049_T|C, 2093_T|C, 2233_A|G, 2375_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A,
3338_T|C, 3395_T|A, 3460_G|A, 3518_C|T, 3534_G|A, 3731_C|T, 4445_C|T, 4619_T|A, 4688_A|G, 4757_T|C, 5303_T|C, 5693_T|C, 5937_T|C, 6422_T|C, 6492_C|T, 6983_A|G, 7043_T|C, 7247_G|A, 7451_A|C,
7517_C|T, 7633_T|C, 7805_T|C, 8007_G|A, 8162_C|T, 8408_T|C, 8765_C|T, 9305_C|T, 9353_T|C, 9434_A|G, 9538_A|G, 9612_T|C, 9676_A|G, 9785_A|G, 10392_A|G, 10561_T|C
 Case 3 (A.1): KX117076.1




Target: 995 samples       Number of changes: 53                                                   


BC: A.1 + A.1             BC BR: 47-48                   BC BR coord: 9439 - 9440          


Direction L1: >>          Initial region span: 1-36,48-53Gap history (edge excluded): 36-48


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 2.95e-05                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 36 1.802575 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 48 0.088061 None None None * * *



Target sequence

, 8_9, 254_A|G, 266_T|C, 433_G|A, 806_C|T, 1175_A|G, 1616_C|T, 2049_T|C, 2093_T|C, 2233_A|G, 2375_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A,
3332_G|A, 3338_T|C, 3460_G|A, 3518_C|T, 3534_G|A, 3731_C|T, 4445_C|T, 4619_T|A, 4757_T|C, 5303_T|C, 5693_T|C, 5937_T|C, 6422_T|C, 6492_C|T, 6983_A|G, 7043_T|C, 7247_G|A, 7451_A|C, 7517_C|T,
7633_T|C, 7805_T|C, 8007_G|A, 8162_C|T, 8408_T|C, 8765_C|T, 9305_C|T, 9353_T|C, 9434_A|G, 9538_A|G, 9612_T|C, 9676_A|G, 9785_A|G, 10392_A|G, 10561_T|C
 Case 3 (A.1): KU922923.1




Target: 995 samples          Number of changes: 44                                                               


BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 9-10, 40-41                  BC BR coord: 1990 - 1991, 9304 - 9305    


Direction L1: >>             Initial region span: 1-5,34-40,41-44Gap history (edge excluded): 5-41 -> 5-34


Alt. candidates: [], []                                                                                                 


Model 1BP/2BP comparison:    2BP vs 1BP: 6.21e-37                                                                       


Rec. model vs L1: 2.43e-57   Rec. model vs L2: 1.44e-03                                                          


Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 5 9.392444 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 34 0.736746 NaN NaN NaN * * *
A.1.NmC1 181 41 0.000000 -170.678084 479.356168 3.980060e-74
A.1.NmC2 83 41 -1.529105 -87.040820 312.081640 8.400015e-38
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 41 2.741564 None None None * * *



Target sequence

, 254_A|G, 428_T|A, 755_T|C, 875_C|T, 881_G|T, 902_T|G, 967_C|T, 1398_C|T, 1616_C|T, 2006_T|C, 2375_C|T, 2534_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3170_G|A, 3186_G|A,
3218_T|A, 3332_G|A, 3459_C|T, 3534_G|A, 3731_C|T, 3784_T|C, 3902_C|T, 3989_T|C, 4268_C|T, 4448_T|C, 4930_C|A, 5937_T|C, 6008_C|T, 6983_A|G, 7196_G|A, 7451_A|C, 7633_T|C, 7805_T|C, 8534_C|A,
9196_G|T, 9209_A|G, 9305_C|T, 9353_T|C, 10164_A|G, 10561_T|C
 Case 3 (A.1): KU922960.1




Target: 995 samples          Number of changes: 43                                                               


BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 8-9, 39-40                   BC BR coord: 1990 - 1991, 9304 - 9305    


Direction L1: >>             Initial region span: 1-8,33-39,40-43Gap history (edge excluded): 8-40 -> 8-33


Alt. candidates: [], []                                                                                                 


Model 1BP/2BP comparison:    2BP vs 1BP: 2.27e-37                                                                       


Rec. model vs L1: 2.43e-57   Rec. model vs L2: 2.94e-09                                                          


Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 8 11.751824 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 33 0.736746 NaN NaN NaN * * *
A.1.NmC1 181 40 0.000000 -170.678084 479.356168 3.980060e-74
A.1.NmC2 83 40 -1.529105 -87.040820 312.081640 8.400015e-38
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 40 2.741564 None None None * * *



Target sequence

, 254_A|G, 428_T|A, 755_T|C, 875_C|T, 881_G|T, 902_T|G, 1398_C|T, 1616_C|T, 2006_T|C, 2375_C|T, 2534_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3170_G|A, 3186_G|A, 3218_T|A,
3332_G|A, 3459_C|T, 3534_G|A, 3731_C|T, 3784_T|C, 3902_C|T, 3989_T|C, 4268_C|T, 4448_T|C, 4930_C|A, 5937_T|C, 6008_C|T, 6983_A|G, 7196_G|A, 7451_A|C, 7633_T|C, 7805_T|C, 8534_C|A, 9196_G|T,
9209_A|G, 9305_C|T, 9353_T|C, 10164_A|G, 10561_T|C
 Case 3 (A.1): KU955590.1




Target: 995 samples       Number of changes: 49                                                                  


BC: A.1 + A.1.NmC2 + A.1  BC BR: 42-43, 45-46                  BC BR coord: 9295 - 9296, 9433 - 9434      


Direction L1: >>          Initial region span: 1-42,43-45,47-49Gap history (edge excluded): 42-47 -> 45-47


Alt. candidates: [], []                                                                                                 


Model 1BP/2BP comparison: 2BP vs 1BP: 4.68e-01                                                                          


Rec. model vs L1: 4.70e-01Rec. model vs L2: 7.77e-184                                                            


Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 42 4.328234 None None None * * *
|||||

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 45 1.603743 NaN NaN NaN * * *
A.1 995 43 -0.127338 -0.154713 6.309426 0.172045 *
A.1.NmC1 181 45 -9.888850 -9.888850 25.777699 0.000010 * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 47 0.372598 None None None * * *



Target sequence

, 254_A|G, 767_C|T, 1040_T|C, 1475_G|A, 1616_C|T, 1658_T|A, 1814_T|A, 1904_C|T, 2375_C|T, 2549_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A,
3566_T|C, 3731_C|T, 3960_A|G, 3999_T|C, 4001_G|A, 5315_A|G, 5435_C|T, 5480_C|T, 5937_T|C, 6071_C|T, 6599_G|A, 6671_T|C, 6878_C|T, 6983_A|G, 7094_T|C, 7451_A|C, 7633_T|C, 7805_T|C, 7868_G|T,
8207_T|C, 8467_T|C, 9107_A|G, 9242_C|T, 9296_C|T, 9305_C|T, 9353_T|C, 9809_C|T, 10094_A|G, 10319_C|T, 10561_T|C
 Case 3 (A.1): MF167360.1




Target: 995 samples       Number of changes: 50                                                                  


BC: A.1 + A.1.NmC2 + A.1  BC BR: 43-44, 46-47                  BC BR coord: 9295 - 9296, 9433 - 9434      


Direction L1: >>          Initial region span: 1-43,44-46,48-50Gap history (edge excluded): 43-48 -> 46-48


Alt. candidates: [], []                                                                                                 


Model 1BP/2BP comparison: 2BP vs 1BP: 4.68e-01                                                                          


Rec. model vs L1: 4.70e-01Rec. model vs L2: 3.25e-191                                                            


Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 43 4.543362 None None None * * *
|||||

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 46 1.603743 NaN NaN NaN * * *
A.1 995 44 -0.127338 -0.154713 6.309426 0.172045 *
A.1.NmC1 181 46 -9.888850 -9.888850 25.777699 0.000010 * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 48 0.372598 None None None * * *



Target sequence

, 254_A|G, 767_C|T, 1040_T|C, 1475_G|A, 1616_C|T, 1658_T|A, 1814_T|A, 1904_C|T, 2343_T|C, 2375_C|T, 2549_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A,
3534_G|A, 3566_T|C, 3731_C|T, 3960_A|G, 3999_T|C, 4001_G|A, 5315_A|G, 5435_C|T, 5480_C|T, 5937_T|C, 6071_C|T, 6599_G|A, 6671_T|C, 6878_C|T, 6983_A|G, 7094_T|C, 7451_A|C, 7633_T|C, 7805_T|C,
7868_G|T, 8207_T|C, 8467_T|C, 9107_A|G, 9242_C|T, 9296_C|T, 9305_C|T, 9353_T|C, 9809_C|T, 10094_A|G, 10319_C|T, 10561_T|C
 Case 3 (A.1): KY379148.1




Target: 995 samples       Number of changes: 50                                                                  


BC: A.1 + A.1.NmC2 + A.1  BC BR: 43-44, 46-47                  BC BR coord: 9295 - 9296, 9433 - 9434      


Direction L1: >>          Initial region span: 1-43,44-46,48-50Gap history (edge excluded): 43-48 -> 46-48


Alt. candidates: [], []                                                                                                 


Model 1BP/2BP comparison: 2BP vs 1BP: 4.68e-01                                                                          


Rec. model vs L1: 4.70e-01Rec. model vs L2: 1.24e-191                                                            


Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 43 4.563565 None None None * * *
|||||

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 46 1.603743 NaN NaN NaN * * *
A.1 995 44 -0.127338 -0.154713 6.309426 0.172045 *
A.1.NmC1 181 46 -9.888850 -9.888850 25.777699 0.000010 * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 48 0.372598 None None None * * *



Target sequence

, 254_A|G, 767_C|T, 1040_T|C, 1475_G|A, 1616_C|T, 1658_T|A, 1814_T|A, 1904_C|T, 2375_C|T, 2549_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A,
3566_T|C, 3593_T|C, 3731_C|T, 3960_A|G, 3999_T|C, 4001_G|A, 5315_A|G, 5435_C|T, 5480_C|T, 5937_T|C, 6071_C|T, 6599_G|A, 6671_T|C, 6878_C|T, 6983_A|G, 7094_T|C, 7451_A|C, 7633_T|C, 7805_T|C,
7868_G|T, 8207_T|C, 8467_T|C, 9107_A|G, 9242_C|T, 9296_C|T, 9305_C|T, 9353_T|C, 9809_C|T, 10094_A|G, 10319_C|T, 10561_T|C
 Case 3 (A.1): PP431236.1




Target: 995 samples        Number of changes: 29                                             


BC: A.1 + A.1.NmC2         BC BR: 25-26                   BC BR coord: 9016 - 9017    


Direction L1: <<           Initial region span: 1-25,26-29Gap history (edge excluded):


Alt. candidates: [], []                                                                             


Model 1BP/2BP comparison:  -                                                                        


Rec. model vs L1: 2.63e-01 Rec. model vs L2: 4.77e-65                                        


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 25 1.359142 None None None * * *
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 26 2.741564 NaN NaN NaN * * *
A.1 995 3 0.157890 -1.248231 12.496462 0.085435 *



Target sequence

, 254_A|G, 1616_C|T, 1875_T|C, 2375_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 2948_T|C, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3731_C|T, 3797_A|G, 4988_G|T, 5768_G|A, 5937_T|C, 6470_G|C,
6890_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 8570_T|C, 8867_C|T, 9305_C|T, 9353_T|C, 10164_A|G, 10561_T|C
 Case 3 (A.1): KY120352.1




Target: 995 samples       Number of changes: 34                                                 


BC: A.1 + A.1             BC BR: 18-19                  BC BR coord: 4999 - 5000         


Direction L1: <<          Initial region span: 1-7,24-34Gap history (edge excluded): 7-24


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 5.72e-19                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 7 0.499275 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 24 1.386952 None None None * * *



Target sequence

, 254_A|G, 1167_T|A, 1616_C|T, 2681_G|A, 2717_C|T, 2724_T|C, 2768_A|G, 2925_G|A, 3059_G|A, 3137_TC|CT, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3497_G|A, 3731_C|T, 3911_A|G, 4757_T|C,
5387_C|T, 5420_T|C, 5937_T|C, 7451_A|C, 7511_C|T, 7514_A|C, 7633_T|C, 7805_T|C, 8045_T|C, 8207_T|C, 8250_C|T, 9244_T|C, 9305_C|T, 9353_T|C, 9553_A|G, 9908_A|G
 Case 3 (A.1): KY553111.1




Target: 995 samples       Number of changes: 243                                                 


BC: A.1 + A.1             BC BR: 18-19                   BC BR coord: 754 - 755           


Direction L1: <<          Initial region span: 1-9,32-243Gap history (edge excluded): 9-32


Alt. candidates: [], []                                                                                 


Model 1BP/2BP comparison: 1BP vs 2BP: 3.98e-14                                                          


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                             


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 9 0.055838 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 32 13.880017 None None None * * *



Target sequence

, 227_T|C, 254_A|G, 257_T|A, 428_T|C, 434_T|C, 446_T|C, 455_G|C, 467_T|C, 475_C|T, 523_A|G, 558_T|C, 578_T|C, 584_G|A, 614_C|T, 639_C|T, 653_G|A, 689_G|A, 719_T|C, 803_A|G, 806_C|T, 837_T|C,
851_A|G, 872_T|C, 917_C|T, 941_C|T, 1043_T|C, 1070_C|T, 1175_A|G, 1214_A|G, 1232_A|G, 1304_C|A, 1433_1438, 1440_1445, 1587_T|C, 1592_T|C, 1616_C|T, 1655_C|T, 1670_C|T, 1682_C|T, 1871_T|C,
1904_C|T, 1910_G|A, 2021_C|T, 2066_C|T, 2084_T|C, 2141_C|T, 2375_C|T, 2394_A|G, 2411_C|T, 2435_T|C, 2437_TG|CA, 2447_C|T, 2525_G|A, 2606_C|T, 2613_T|C, 2625_G|A, 2648_T|G, 2669_T|C, 2681_G|A,
2714_C|T, 2724_T|C, 2768_A|G, 2846_G|A, 2925_G|A, 3038_T|C, 3053_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3275_C|T, 3332_G|A, 3347_C|T, 3362_T|C,
3365_A|G, 3380_T|C, 3434_G|A, 3534_G|A, 3545_A|G, 3701_T|C, 3721_TT|CC, 3731_C|T, 3794_C|T, 3797_A|G, 3806_A|T, 3854_A|G, 3885_T|C, 3905_C|T, 3938_T|C, 3989_T|C, 4031_C|T, 4070_T|A, 4085_T|C,
4128_T|C, 4146_C|T, 4238_C|T, 4271_A|G, 4277_T|C, 4295_A|G, 4422_G|A, 4439_C|T, 4454_G|A, 4472_T|C, 4481_G|A, 4493_C|T, 4502_C|T, 4523_G|A, 4544_T|C, 4592_A|G, 4595_C|T, 4607_A|G, 4706_A|T,
4733_T|C, 4751_T|C, 4838_T|C, 4859_A|G, 4871_T|C, 4988_G|A, 5000_T|C, 5024_T|C, 5060_T|C, 5066_C|T, 5193_T|C, 5279_A|G, 5336_G|T, 5369_C|T, 5375_A|G, 5387_C|T, 5429_G|A, 5450_T|C, 5492_A|C,
5591_T|C, 5612_T|C, 5717_C|T, 5744_A|G, 5807_A|G, 5811_C|A, 5828_T|C, 5846_T|C, 5888_T|C, 5901_C|T, 5937_T|C, 5975_C|T, 6056_C|T, 6092_C|T, 6101_T|C, 6164_C|T, 6239_T|G, 6246_C|T, 6310_C|T,
6362_AC|GT, 6431_G|A, 6443_G|A, 6458_G|A, 6473_T|C, 6593_C|T, 6684_A|C, 6698_A|G, 6746_C|T, 6797_T|C, 6890_A|G, 6983_A|G, 7025_C|T, 7037_C|T, 7049_CT|TC, 7085_A|G, 7139_A|G, 7157_C|T,
7202_A|G, 7208_A|G, 7313_T|G, 7427_A|G, 7451_A|C, 7517_C|T, 7529_T|C, 7568_T|C, 7586_T|C, 7633_T|C, 7646_C|T, 7679_A|G, 7713_T|C, 7805_T|C, 7817_G|A, 7853_G|T, 7869_C|A, 7871_G|A, 7883_G|A,
7899_A|G, 7913_T|C, 7937_C|T, 7961_A|G, 7994_T|C, 8006_CG|TA, 8093_G|T, 8291_A|G, 8408_T|C, 8504_T|C, 8516_A|G, 8606_C|T, 8732_T|C, 8813_G|A, 8832_C|A, 9011_C|T, 9017_T|C, 9119_T|C, 9176_C|T,
9206_A|G, 9212_A|G, 9272_C|T, 9305_C|T, 9353_T|C, 9407_G|A, 9434_A|G, 9455_G|A, 9503_C|T, 9509_T|C, 9518_A|G, 9527_A|G, 9591_T|C, 9596_G|A, 9677_G|A, 9731_A|G, 9818_G|A, 9884_G|A, 9893_C|A,
9896_T|A, 9899_A|G, 10001_C|T, 10133_G|A, 10166_G|A, 10244_C|T, 10262_T|C, 10268_C|T, 10281_G|A, 10334_A|G, 10361_T|C, 10392_A|G, 10561_T|C, 10566_T|A
 Case 3 (A.1): PP431225.1




Target: 995 samples        Number of changes: 18                                                 


BC: A.1.NmC2 + A.1         BC BR: 12-13                  BC BR coord: 2731 - 2732         


Direction L1: >>           Initial region span: 1-7,14-18Gap history (edge excluded): 7-14


Alt. candidates: [], []                                                                                 


Model 1BP/2BP comparison:  -                                                                            


Rec. model vs L1: 2.87e-15 Rec. model vs L2: 9.63e-02                                            


Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 7 11.865805 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 14 0.357799 None None None * * *



Target sequence

, 254_A|G, 428_T|A, 755_T|C, 875_C|T, 881_G|T, 1398_C|T, 1616_C|T, 1922_C|T, 2375_C|T, 2534_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3026_T|C, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A
 Case 3 (A.1): MW915411.1




Target: 995 samples        Number of changes: 93                                                 


BC: A.1 + A.1.NmC1         BC BR: 90-91                  BC BR coord: 10288 - 10289       


Direction L1: <<           Initial region span: 1-4,91-93Gap history (edge excluded): 4-91


Alt. candidates: [], []                                                                                 


Model 1BP/2BP comparison:  -                                                                            


Rec. model vs L1: 1.81e+00 Rec. model vs L2: 3.55e-289                                           


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 4 0.670399 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 91 3.420355 None None None * * *



Target sequence

, 19_A|G, 233_G|A, 254_A|G, 512_C|T, 523_A|G, 558_T|C, 579_A|G, 653_G|A, 716_C|T, 902_T|C, 1145_A|G, 1175_A|G, 1358_G|A, 1515_C|T, 1538_A|G, 1568_C|T, 1616_C|T, 1748_T|C, 1760_A|G, 2375_C|T,
2648_T|C, 2654_C|T, 2681_G|A, 2724_T|C, 2894_G|T, 2925_G|A, 2936_A|G, 3035_C|T, 3059_G|A, 3134_C|T, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3248_T|C, 3254_T|C, 3311_A|G, 3332_G|A, 3455_G|A,
3482_T|C, 3518_C|T, 3534_G|A, 3731_C|T, 3902_C|T, 4085_T|C, 4454_G|A, 4472_T|C, 4499_C|A, 5000_T|C, 5060_T|C, 5375_A|G, 5516_T|C, 5564_C|T, 5828_T|C, 5937_T|C, 5975_C|T, 6056_C|T, 6140_A|G,
6254_T|C, 6269_C|T, 6308_C|T, 6363_C|T, 6629_T|C, 6698_A|G, 6731_G|A, 6917_T|C, 6981_G|A, 6983_A|G, 6996_T|C, 7014_C|T, 7271_C|T, 7293_C|T, 7451_A|C, 7633_T|C, 7805_T|C, 8007_G|A, 8045_T|C,
8408_T|C, 8414_G|A, 8477_T|A, 9017_T|C, 9305_C|T, 9344_G|A, 9353_T|C, 9434_A|G, 9569_A|G, 9596_G|A, 9757_A|G, 9866_A|G, 10223_C|T, 10392_A|G, 10477_T|C, 10561_T|C
 Case 3 (A.1): PP431239.1




Target: 995 samples          Number of changes: 36                                                               


BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 5-6, 25-26                   BC BR coord: 1174 - 1175, 5936 - 5937    


Direction L1: >>             Initial region span: 1-5,22-25,26-36Gap history (edge excluded): 5-26 -> 5-22


Alt. candidates: [], []                                                                                                 


Model 1BP/2BP comparison:    2BP vs 1BP: 2.84e-24                                                                       


Rec. model vs L1: 7.75e-38   Rec. model vs L2: 4.29e-10                                                          


Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 5 9.392444 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 22 0.778802 NaN NaN NaN * * *
A.1.NmC2 83 26 0.000000 -54.652550 211.305099 2.820861e-24
A.1.NmC1 181 26 -1.741599 -93.942486 289.884973 2.449757e-41
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 26 6.356741 None None None * * *



Target sequence

, 254_A|G, 428_T|A, 755_T|C, 875_C|T, 881_G|T, 1616_C|T, 2057_C|T, 2375_C|T, 2534_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3731_C|T,
3902_C|T, 3989_T|C, 4571_T|C, 4988_G|T, 5072_G|A, 5549_C|T, 5937_T|C, 6008_C|T, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9305_C|T, 9353_T|C, 10164_A|G, 10410_G|A, 10561_T|C
 Case 3 (A.1): MT439642.1




Target: 995 samples       Number of changes: 45                                                   


BC: A.1 + A.1             BC BR: 30-31                   BC BR coord: 6007 - 6008          


Direction L1: >>          Initial region span: 1-29,38-45Gap history (edge excluded): 29-38


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 1.29e-10                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 29 3.305789 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 38 1.094003 None None None * * *



Target sequence

, 80, 116_C|A, 138, 254_A|G, 737_A|T, 1434_1445, 1616_C|T, 2375_C|T, 2511_T|A, 2681_G|A, 2724_T|C, 3059_G|A, 3113_C|T, 3140_A|G, 3170_G|A, 3186_G|A, 3218_T|A, 3332_G|A, 3731_C|T, 4152_C|T,
4184_C|T, 4271_A|G, 4287_G|A, 4318_T|C, 4530_C|T, 4625_A|G, 4658_G|A, 4682_C|T, 5718_G|A, 5937_T|C, 6104_T|C, 6353_G|A, 6983_A|G, 7340_C|T, 7451_A|C, 7633_T|C, 7805_T|C, 8714_G|A, 8783_T|C,
9305_C|T, 9353_T|C, 10265_A|G, 10500_G|A, 10539_G|A, 10561_T|C
 Case 3 (A.1): PP431229.1




Target: 995 samples          Number of changes: 39                                                             


BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 3-4, 33-34                 BC BR coord: 652 - 653, 7651 - 7652      


Direction L1: <<             Initial region span: 1-3,4-5,35-39Gap history (edge excluded): 3-35 -> 5-35


Alt. candidates: [], []                                                                                               


Model 1BP/2BP comparison:    2BP vs 1BP: 1.95e-12                                                                     


Rec. model vs L1: 1.48e-23   Rec. model vs L2: 2.94e-03                                                        


Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 3 2.657647 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 5 0.470661 NaN NaN NaN * * *
A.1.NmC2 83 4 0.000000 -33.869168 205.738336 1.936769e-12 *
A.1.NmC1 181 4 -1.588178 -171.846304 481.692608 2.318978e-72 *
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 35 3.669037 None None None * * *



Target sequence

, 254_A|G, 428_T|A, 575_T|C, 727_A|G, 736_C|T, 755_T|C, 875_C|T, 881_G|T, 902_T|G, 1398_C|T, 1616_C|T, 2375_C|T, 2534_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A,
3218_T|A, 3332_G|A, 3459_C|T, 3534_G|A, 3557_T|C, 3731_C|T, 3989_T|C, 5450_T|C, 5937_T|C, 6008_C|T, 6983_A|G, 7451_A|C, 7568_T|C, 7633_T|C, 7805_T|C, 9305_C|T, 9353_T|C, 10164_A|G, 10378_A|G,
10561_T|C
 Case 3 (A.1): KY559009.1




Target: 995 samples       Number of changes: 36                                                 


BC: A.1 + A.1             BC BR: 6-7                    BC BR coord: 1990 - 1991         


Direction L1: <<          Initial region span: 1-4,20-36Gap history (edge excluded): 4-20


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 2.52e-02                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 4 0.686929 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 20 1.960004 None None None * * *



Target sequence

, 254_A|G, 1364_C|T, 1511_C|T, 1587_T|C, 1616_C|T, 1838_C|T, 2375_C|T, 2648_T|C, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3731_C|T, 3771_C|T,
4152_C|T, 4287_G|A, 5937_T|C, 6269_C|T, 6353_G|A, 6804_C|T, 6983_A|G, 7268_G|A, 7451_A|C, 7633_T|C, 7805_T|C, 8714_G|A, 8991_C|T, 9020_T|C, 9305_C|T, 9353_T|C, 10367_T|C
 Case 3 (A.1): LC191864.1




Target: 995 samples       Number of changes: 69                                                   


BC: A.1 + A.1             BC BR: 48-49                   BC BR coord: 7049 - 7050          


Direction L1: >>          Initial region span: 1-48,58-69Gap history (edge excluded): 48-58


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 7.16e-07                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 48 3.611924 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 58 0.173495 None None None * * *



Target sequence

, 19_A|G, 254_A|G, 433_G|A, 685_C|T, 1175_A|G, 1322_A|C, 1616_C|T, 1772_T|C, 2066_C|T, 2189_C|T, 2375_C|T, 2420_T|C, 2555_T|C, 2603_C|T, 2609_T|C, 2613_T|C, 2654_C|T, 2681_G|A, 2702_A|G,
2724_T|C, 2925_G|A, 2930_T|C, 3002_T|C, 3030_C|T, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3338_T|C, 3518_C|T, 3534_G|A, 3731_C|T, 3776_G|T, 3851_T|C, 4688_A|G, 5003_C|T, 5363_C|T,
5519_A|G, 5612_T|C, 5937_T|C, 6038_T|C, 6422_T|C, 6492_C|T, 6860_C|T, 6983_A|G, 7007_C|T, 7043_T|C, 7451_A|C, 7517_C|T, 7547_G|T, 7633_T|C, 7805_T|C, 8007_G|A, 8123_T|C, 8408_T|C, 8528_T|C,
8887_A|G, 8895_T|C, 9305_C|T, 9353_T|C, 9359_C|T, 9392_A|T, 9404_A|G, 9434_A|G, 9538_A|G, 10370_A|G, 10392_A|G, 10561_T|C
 Case 3 (A.1): OL423654.1




Target: 995 samples       Number of changes: 35                                                   


BC: A.1 + A.1             BC BR: 25-26                   BC BR coord: 7516 - 7517          


Direction L1: >>          Initial region span: 1-23,28-35Gap history (edge excluded): 23-28


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 2.57e-07                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 23 2.169111 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 28 0.487976 None None None * * *



Target sequence

, 254_A|G, 1616_C|T, 2681_G|A, 2717_C|T, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3431_G|A, 3712_A|G, 3731_C|T, 3999_T|G, 4172_C|T, 4390_C|T, 5315_A|G, 5460_A|C,
5691_G|A, 5937_T|C, 6311_G|A, 7046_T|C, 7050_T|C, 7451_A|C, 7633_T|C, 7805_T|C, 8045_T|C, 8075_G|A, 8534_C|T, 8774_A|G, 8945_T|C, 9305_C|T, 9344_G|A, 9353_T|C
 Case 3 (A.1): MT377498.1




Target: 995 samples       Number of changes: 161                                                             


BC: A.1 + A.1.NmC1 + A.1  BC BR: 5-6, 9-10                   BC BR coord: 522 - 523, 754 - 755        


Direction L1: <<          Initial region span: 1-5,6-8,96-161Gap history (edge excluded): 5-96 -> 8-96


Alt. candidates: [], []                                                                                             


Model 1BP/2BP comparison: 2BP vs 1BP: 3.78e-02                                                                      


Rec. model vs L1: 1.39e-02Rec. model vs L2: 0.00e+00                                                         


Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 5 0.679513 None None None * * *
|||||

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 8 4.667316 NaN NaN NaN * * *
A.1 995 77 -0.641906 -2.560621 13.121243 5.117957e-03 *
A.1.NmC2 83 6 -10.000000 -40.000000 88.000000 2.812621e-19
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 96 2.393317 None None None * * *



Target sequence

, 254_A|G, 423_G|A, 428_T|C, 467_T|C, 476_G|A, 523_A|G, 558_T|C, 653_G|A, 719_T|C, 773_T|C, 803_A|G, 884_A|G, 974_C|T, 1046_T|C, 1175_A|G, 1328_T|C, 1391_G|A, 1520_G|A, 1526_T|C, 1592_T|C,
1616_C|T, 1718_C|T, 1748_T|C, 1763_A|G, 1875_T|C, 1896_T|C, 1922_C|T, 2057_C|T, 2066_C|T, 2148_G|A, 2375_C|T, 2411_C|T, 2436_A|G, 2471_A|G, 2519_G|A, 2522_G|A, 2525_G|A, 2576_G|A, 2606_C|T,
2648_T|G, 2681_G|A, 2724_T|C, 2846_G|A, 2925_G|A, 2951_T|C, 2969_C|T, 3008_A|G, 3014_T|C, 3038_T|C, 3059_G|A, 3089_C|T, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C,
3266_C|T, 3332_G|A, 3534_G|A, 3665_G|A, 3731_C|T, 3869_CT|TC, 3885_T|C, 3977_T|C, 3989_T|C, 3992_C|T, 4010_G|A, 4031_C|T, 4085_T|C, 4106_A|G, 4238_C|T, 4244_A|G, 4295_A|G, 4403_A|G, 4445_C|T,
4454_G|T, 4493_C|T, 4523_G|A, 4562_C|T, 4595_C|T, 4733_T|C, 4943_G|A, 4961_T|C, 5000_T|C, 5003_C|T, 5060_T|C, 5210_G|A, 5369_C|T, 5375_A|G, 5387_C|T, 5546_T|C, 5591_T|C, 5744_A|G, 5828_T|C,
5867_T|C, 5937_T|C, 6101_T|C, 6119_C|T, 6155_A|G, 6164_C|T, 6230_A|G, 6233_T|C, 6275_A|T, 6278_C|T, 6473_T|A, 6645_C|T, 6684_A|C, 6807_T|C, 6851_C|T, 6890_A|G, 6911_C|T, 6935_G|A, 6938_A|G,
6983_A|G, 7037_C|T, 7043_T|C, 7049_CT|TC, 7079_A|G, 7151_T|C, 7358_T|C, 7451_A|C, 7517_C|T, 7633_T|C, 7805_T|C, 7811_G|A, 7886_C|T, 7964_A|G, 8007_G|A, 8105_C|T, 8408_T|C, 8516_A|G, 8606_C|T,
8787_G|A, 8852_T|C, 9017_T|C, 9110_G|A, 9206_A|G, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9503_C|T, 9527_A|G, 9557_T|C, 9671_T|A, 9797_T|C, 9881_C|T, 9935_A|G, 10052_T|C, 10127_T|C,
10165_C|T, 10275_A|C, 10361_T|C, 10376_G|A, 10392_A|G, 10477_T|C, 10513_C|T, 10561_T|C, 10613_C|T
 Case 3 (A.1): KY120353.1




Target: 995 samples       Number of changes: 238                                                 


BC: A.1 + A.1             BC BR: 31-32                   BC BR coord: 1397 - 1398         


Direction L1: <<          Initial region span: 1-9,32-238Gap history (edge excluded): 9-32


Alt. candidates: [], []                                                                                 


Model 1BP/2BP comparison: 1BP vs 2BP: 1.97e-15                                                          


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                             


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 9 0.055838 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 32 13.982248 None None None * * *



Target sequence

, 227_T|C, 254_A|G, 257_T|A, 428_T|C, 434_T|C, 446_T|C, 455_G|C, 467_T|C, 475_C|T, 523_A|G, 558_T|C, 578_T|C, 584_G|A, 614_C|T, 639_C|T, 653_G|A, 689_G|A, 719_T|C, 803_A|G, 806_C|T, 837_T|C,
851_A|G, 872_T|C, 917_C|T, 941_C|T, 1043_T|C, 1070_C|T, 1175_A|G, 1214_A|G, 1232_A|G, 1304_C|A, 1587_T|C, 1592_T|C, 1616_C|T, 1655_C|T, 1670_C|T, 1682_C|T, 1871_T|C, 1904_C|T, 1910_G|A,
2021_C|T, 2066_C|T, 2084_T|C, 2141_C|T, 2375_C|T, 2394_A|G, 2411_C|T, 2435_T|C, 2437_TG|CA, 2447_C|T, 2525_G|A, 2606_C|T, 2613_T|C, 2625_G|A, 2648_T|G, 2669_T|C, 2681_G|A, 2714_C|T, 2724_T|C,
2768_A|G, 2846_G|A, 2925_G|A, 3038_T|C, 3053_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3275_C|T, 3332_G|A, 3347_C|T, 3362_T|C, 3365_A|G, 3380_T|C,
3434_G|A, 3534_G|A, 3545_A|G, 3701_T|C, 3721_TT|CC, 3731_C|T, 3797_A|G, 3806_A|T, 3854_A|G, 3885_T|C, 3905_C|T, 3938_T|C, 3989_T|C, 4031_C|T, 4070_T|A, 4085_T|C, 4128_T|C, 4146_C|T, 4238_C|T,
4271_A|G, 4277_T|C, 4295_A|G, 4422_G|A, 4439_C|T, 4454_G|A, 4472_T|C, 4481_G|A, 4493_C|T, 4502_C|T, 4523_G|A, 4544_T|C, 4592_A|G, 4595_C|T, 4607_A|G, 4706_A|T, 4733_T|C, 4751_T|C, 4838_T|C,
4859_A|G, 4871_T|C, 4933_G|T, 4988_G|A, 5000_T|C, 5024_T|C, 5060_T|C, 5066_C|T, 5193_T|C, 5279_A|G, 5336_G|T, 5369_C|T, 5375_A|G, 5387_C|T, 5429_G|A, 5450_T|C, 5492_A|C, 5591_T|C, 5612_T|C,
5717_C|T, 5744_A|G, 5807_A|G, 5811_C|A, 5828_T|C, 5846_T|C, 5888_T|C, 5901_C|T, 5937_T|C, 5975_C|T, 6056_C|T, 6092_C|T, 6101_T|C, 6164_C|T, 6239_T|G, 6246_C|T, 6310_C|T, 6362_AC|GT, 6431_G|A,
6443_G|A, 6458_G|A, 6473_T|C, 6593_C|T, 6684_A|C, 6698_A|G, 6746_C|T, 6797_T|C, 6890_A|G, 6983_A|G, 7025_C|T, 7037_C|T, 7049_CT|TC, 7085_A|G, 7139_A|G, 7157_C|T, 7202_A|G, 7208_A|G, 7313_T|G,
7427_A|G, 7451_A|C, 7517_C|T, 7529_T|C, 7568_T|C, 7586_T|C, 7633_T|C, 7646_C|T, 7679_A|G, 7713_T|C, 7805_T|C, 7817_G|A, 7853_G|T, 7869_C|A, 7871_G|A, 7883_G|A, 7899_A|G, 7913_T|C, 7937_C|T,
7961_A|G, 7994_T|C, 8006_CG|TA, 8093_G|T, 8291_A|G, 8408_T|C, 8504_T|C, 8516_A|G, 8606_C|T, 8732_T|C, 8813_G|A, 8832_C|A, 9011_C|T, 9017_T|C, 9119_T|C, 9176_C|T, 9206_A|G, 9212_A|G, 9272_C|T,
9305_C|T, 9353_T|C, 9407_G|A, 9434_A|G, 9455_G|A, 9503_C|T, 9509_T|C, 9518_A|G, 9527_A|G, 9591_T|C, 9596_G|A, 9677_G|A, 9731_A|G, 9818_G|A, 9884_G|A, 9893_C|A, 9896_T|A, 9899_A|G, 10001_C|T,
10133_G|A, 10166_G|A, 10244_C|T, 10262_T|C, 10268_C|T, 10281_G|A, 10334_A|G, 10361_T|C
 Case 3 (A.1): PP431246.1




Target: 995 samples        Number of changes: 32                                             


BC: A.1 + A.1.NmC2         BC BR: 28-29                   BC BR coord: 9016 - 9017    


Direction L1: <<           Initial region span: 1-28,29-32Gap history (edge excluded):


Alt. candidates: [], []                                                                             


Model 1BP/2BP comparison:  -                                                                        


Rec. model vs L1: 2.63e-01 Rec. model vs L2: 4.06e-91                                        


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 28 2.094844 None None None * * *
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 29 2.741564 NaN NaN NaN * * *
A.1 995 2 0.865675 -1.248231 12.496462 0.085435 *



Target sequence

, 254_A|G, 428_T|C, 1298_T|C, 1616_C|T, 1875_T|C, 2375_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3731_C|T, 4988_G|T, 5180_A|G, 5243_T|A, 5549_C|T,
5768_G|A, 5937_T|C, 6890_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 8447_C|T, 8570_T|C, 8867_C|T, 9305_C|T, 9353_T|C, 10164_A|G, 10561_T|C
 Case 3 (A.1): KY785444.1




Target: 995 samples       Number of changes: 18                                                   


BC: A.1 + A.1             BC BR: 13-14                   BC BR coord: 7049 - 7050          


Direction L1: >>          Initial region span: 1-11,14-18Gap history (edge excluded): 11-14


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 8.23e-01                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 11 1.832899 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 14 0.376929 None None None * * *



Target sequence

, 254_A|G, 1052_G|A, 1616_C|T, 1736_A|G, 2375_C|T, 5195_G|A, 5297_C|T, 5315_A|G, 5408_C|T, 6725_T|C, 6737_C|T, 6977_G|T, 6983_A|G, 7226_A|G, 7633_T|C, 7805_T|C, 9353_T|C, 10178_C|T
 Case 3 (A.1): OL423650.1




Target: 995 samples       Number of changes: 49                                                   


BC: A.1 + A.1             BC BR: 12-13                   BC BR coord: 3898 - 3899          


Direction L1: <<          Initial region span: 1-11,14-49Gap history (edge excluded): 11-14


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 7.93e-10                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 11 0.865067 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 14 3.904957 None None None * * *



Target sequence

, 78_T|A, 254_A|G, 1475_G|A, 1616_C|T, 1904_C|T, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3657_A|T, 3731_C|T, 3945_T|C, 4658_G|A, 5156_T|C, 5167_A|G, 5315_A|G, 5746_A|T, 5903_A|G,
5937_T|C, 6983_A|G, 7058_T|C, 7094_T|C, 7451_A|C, 7633_T|C, 7805_T|C, 8144_A|G, 9144_T|C, 9149_C|T, 9242_C|T, 9296_C|T, 9305_C|T, 9353_T|C, 9401_G|A, 10168_A|G, 10220_T|C, 10226_A|G,
10230_C|G, 10234_G|C, 10240_G|C, 10242_A|C, 10245_A|C, 10252_CTG|GAA, 10256_G|A, 10259_C|A, 10261_TT|AA, 10268_C|A, 10271_A|T, 10274_CAAC|GGTG
 Case 3 (A.1): PP431247.1




Target: 995 samples          Number of changes: 42                                                                  


BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 20-21, 37-38                  BC BR coord: 3517 - 3518, 9304 - 9305      


Direction L1: >>             Initial region span: 1-17,36-37,38-42Gap history (edge excluded): 17-38 -> 17-36


Alt. candidates: [], []                                                                                                    


Model 1BP/2BP comparison:    2BP vs 1BP: 1.67e-27                                                                          


Rec. model vs L1: 7.34e-40   Rec. model vs L2: 2.45e-07                                                             


Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 17 14.283815 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 36 0.448682 NaN NaN NaN * * *
A.1.NmC1 181 38 0.000000 -114.044124 318.088248 4.523358e-50
A.1.NmC2 83 38 -1.529105 -62.078579 214.157158 1.673300e-27
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 38 4.767649 None None None * * *



Target sequence

, 254_A|G, 428_T|A, 755_T|C, 875_C|T, 881_G|T, 902_T|G, 1398_C|T, 1616_C|T, 2375_C|T, 2534_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3227_T|G, 3332_G|A,
3459_C|T, 3534_G|A, 3674_T|C, 3731_C|T, 3810_T|C, 3902_C|T, 3989_T|C, 4332_C|T, 4448_T|C, 4970_G|A, 5937_T|C, 6008_C|T, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 8675_G|A, 8696_C|T, 9305_C|T,
9353_T|C, 10164_A|G, 10410_G|A, 10561_T|C
 Case 3 (A.1): KY014315.2




Target: 995 samples       Number of changes: 40                                                 


BC: A.1 + A.1             BC BR: 27-28                  BC BR coord: 6007 - 6008         


Direction L1: <<          Initial region span: 1-7,28-40Gap history (edge excluded): 7-28


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 3.35e-09                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 7 0.310254 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 28 0.571778 None None None * * *



Target sequence

, 138_T|C, 254_A|G, 1616_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3070_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 4016_T|A,
4733_T|C, 4784_G|A, 4905_T|C, 5195_G|A, 5228_T|C, 5315_A|G, 5405_C|T, 5937_T|C, 6327_A|C, 6725_T|C, 6737_C|T, 6962_A|G, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9240_C|T, 9305_C|T, 9353_T|C,
9533_T|C, 10163_T|C
 Case 3 (A.1): PP431233.1




Target: 995 samples          Number of changes: 41                                                               


BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 3-4, 36-37                   BC BR coord: 652 - 653, 9304 - 9305      


Direction L1: <<             Initial region span: 1-3,35-36,37-41Gap history (edge excluded): 3-37 -> 3-35


Alt. candidates: [], []                                                                                                 


Model 1BP/2BP comparison:    2BP vs 1BP: 7.15e-18                                                                       


Rec. model vs L1: 6.88e-36   Rec. model vs L2: 6.46e-04                                                          


Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 3 2.657647 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 35 0.203761 NaN NaN NaN * * *
A.1.NmC1 181 37 0.000000 -170.633219 497.266437 8.900671e-72
A.1.NmC2 83 36 -1.418347 -46.519526 249.039052 7.110209e-18 *
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 37 3.669037 None None None * * *



Target sequence

, 254_A|G, 428_T|A, 575_T|C, 665_C|T, 755_T|C, 770_C|T, 875_C|T, 881_G|T, 902_T|G, 1398_C|T, 1616_C|T, 2375_C|T, 2435_T|C, 2534_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G,
3186_G|A, 3218_T|A, 3332_G|A, 3459_C|T, 3534_G|A, 3731_C|T, 3836_T|C, 3902_C|T, 3989_T|C, 4957_T|C, 5937_T|C, 6008_C|T, 6983_A|G, 7451_A|C, 7633_T|C, 7649_T|C, 7805_T|C, 9305_C|T, 9353_T|C,
10164_A|G, 10378_A|G, 10561_T|C
 Case 3 (A.1): KY014314.2




Target: 995 samples       Number of changes: 46                                                   


BC: A.1 + A.1             BC BR: 19-20                   BC BR coord: 3253 - 3254          


Direction L1: <<          Initial region span: 1-17,23-46Gap history (edge excluded): 17-23


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 9.54e-10                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 17 2.108104 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 23 3.561785 None None None * * *



Target sequence

, 254_A|G, 506_T|C, 1533_C|T, 1616_C|T, 1718_C|A, 1727_C|T, 2060_T|C, 2435_T|C, 2636_C|A, 2681_G|A, 2717_C|T, 2724_T|C, 2861_C|T, 2925_G|A, 3059_G|A, 3140_A|G, 3143_C|T, 3186_G|A, 3218_T|A,
3332_G|A, 3731_C|T, 3899_C|T, 3999_T|C, 5163_C|T, 5249_C|T, 5369_C|T, 5840_T|C, 5937_T|C, 6278_C|T, 6908_T|C, 7451_A|C, 7633_T|C, 7805_T|C, 8045_T|C, 8105_C|T, 8459_G|A, 8621_G|A, 8631_A|G,
8888_T|C, 9029_C|T, 9287_C|T, 9305_C|T, 9311_G|A, 9353_T|C, 10301_T|G, 10561_T|C
 Case 3 (A.1): MH368551.1




Target: 995 samples        Number of changes: 180                                               


BC: A.1 + A.1.NmC1         BC BR: 176-177                    BC BR coord: 10391 - 10392  


Direction L1: >>           Initial region span: 1-176,177-180Gap history (edge excluded):


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison:  -                                                                           


Rec. model vs L1: 6.96e-02 Rec. model vs L2: 0.00e+00                                           


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 176 3.997354 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 177 3.420355 None None None * * *



Target sequence

, 122_A|G, 254_A|G, 359_C|T, 423_G|A, 467_T|C, 475_C|T, 496_G|A, 523_A|G, 558_T|A, 653_G|A, 719_T|C, 798_T|C, 803_A|G, 837_T|C, 1070_C|T, 1175_A|G, 1337_A|T, 1343_C|T, 1442_C|T, 1616_C|T,
1655_C|T, 1736_A|G, 1922_C|T, 2066_C|T, 2093_T|C, 2111_T|G, 2156_G|A, 2282_A|G, 2285_C|T, 2298_T|C, 2375_C|T, 2394_A|G, 2411_C|T, 2525_G|A, 2570_C|T, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A,
2724_T|C, 2828_C|T, 2864_A|G, 2925_G|A, 3038_T|C, 3050_T|C, 3052_T|C, 3059_G|A, 3071_A|G, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3282_A|G, 3296_C|T, 3332_G|A,
3473_C|T, 3518_C|T, 3534_G|A, 3605_G|A, 3617_G|A, 3731_C|T, 3767_A|T, 3806_A|T, 3827_C|T, 3854_A|G, 3885_T|C, 3928_T|C, 3989_T|C, 4085_T|C, 4094_C|T, 4106_A|G, 4238_C|T, 4295_A|G, 4454_G|A,
4481_G|A, 4493_C|T, 4523_G|A, 4536_A|G, 4592_A|G, 4595_C|T, 4733_T|C, 4751_T|C, 4988_G|A, 5000_T|C, 5036_C|T, 5060_T|C, 5066_C|T, 5096_T|C, 5267_T|C, 5369_C|T, 5375_A|G, 5387_C|T, 5561_C|T,
5591_T|C, 5717_C|T, 5828_T|C, 5937_T|C, 6002_T|C, 6056_C|T, 6065_T|C, 6092_C|T, 6101_T|C, 6164_C|T, 6363_C|T, 6443_G|A, 6473_T|C, 6512_C|T, 6533_A|G, 6584_T|C, 6608_G|A, 6626_C|T, 6629_T|C,
6684_A|C, 6746_C|T, 6890_A|G, 6983_A|G, 6989_C|T, 7037_C|T, 7049_CT|TC, 7148_T|C, 7157_C|T, 7175_C|T, 7451_A|T, 7493_G|T, 7517_C|T, 7538_A|G, 7568_T|C, 7577_T|C, 7604_T|C, 7633_T|C, 7679_A|G,
7713_T|C, 7805_T|C, 7826_T|C, 7869_C|A, 7937_C|T, 8007_G|A, 8105_C|T, 8387_C|T, 8408_T|C, 8429_G|A, 8516_A|G, 8597_T|C, 8823_C|T, 8888_T|C, 9017_T|C, 9098_T|C, 9176_C|T, 9200_G|A, 9225_C|T,
9272_C|T, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9503_C|T, 9527_A|G, 9623_C|T, 9677_G|A, 9704_C|T, 9758_A|G, 9884_G|A, 9887_C|T, 9896_T|A, 9899_A|G, 10217_A|G, 10230_C|T, 10281_G|A,
10286_C|T, 10314_A|G, 10349_T|C, 10361_T|C, 10376_G|A, 10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): MW122393.1




Target: 995 samples       Number of changes: 47                                                   


BC: A.1 + A.1             BC BR: 38-39                   BC BR coord: 8311 - 8312          


Direction L1: >>          Initial region span: 1-38,43-47Gap history (edge excluded): 38-43


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 3.66e-07                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 38 4.700514 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 43 0.315947 None None None * * *



Target sequence

, 254_A|G, 346_T|C, 779_T|C, 1187_G|T, 1475_G|A, 1499_A|G, 1616_C|T, 1715_G|A, 1904_C|T, 2375_C|T, 2925_G|A, 3059_G|A, 3140_A|G, 3153_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3566_T|C,
3593_T|C, 3700_G|A, 3731_C|T, 3797_A|G, 4883_C|T, 5087_T|C, 5156_T|C, 5937_T|C, 6536_C|T, 6563_G|A, 6629_T|A, 6671_T|C, 6983_A|G, 7094_T|C, 7151_T|C, 7451_A|C, 7505_C|T, 7633_T|C, 8237_T|C,
8594_C|T, 8852_T|C, 9017_T|C, 9203_A|G, 9242_C|T, 9296_C|T, 9305_C|T, 9353_T|C, 9488_C|T
 Case 3 (A.1): KY693678.1




Target: 995 samples        Number of changes: 49                                                 


BC: A.1.NmC2 + A.1         BC BR: 11-12                  BC BR coord: 2404 - 2405         


Direction L1: >>           Initial region span: 1-8,46-49Gap history (edge excluded): 8-46


Alt. candidates: [], []                                                                                 


Model 1BP/2BP comparison:  -                                                                            


Rec. model vs L1: 1.28e-87 Rec. model vs L2: 3.46e+00                                            


Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 8 11.668796 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 46 0.669623 None None None * * *



Target sequence

, 254_A|G, 428_T|A, 755_T|C, 875_C|T, 881_G|T, 902_T|G, 1398_C|T, 1421_C|T, 1592_T|C, 1616_C|T, 2375_C|T, 2534_C|T, 2558_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A,
3218_T|A, 3332_G|A, 3338_T|C, 3459_C|T, 3534_G|A, 3731_C|T, 3902_C|T, 3989_T|C, 4448_T|C, 4547_C|A, 5937_T|C, 6008_C|T, 6179_C|T, 6422_T|C, 6542_C|T, 6983_A|G, 7310_G|A, 7451_A|C, 7633_T|C,
7805_T|C, 8069_T|C, 8621_G|A, 9305_C|T, 9353_T|C, 9602_G|A, 10164_A|G, 10382_A|T, 10384_C|T, 10390_T|C, 10561_T|C
 Case 3 (A.1): KY765317.1




Target: 995 samples       Number of changes: 49                                                 


BC: A.1 + A.1             BC BR: 9-10                   BC BR coord: 2404 - 2405         


Direction L1: <<          Initial region span: 1-7,10-49Gap history (edge excluded): 7-10


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 4.36e-05                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 7 0.961604 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 10 4.49497 None None None * * *



Target sequence

, 254_A|G, 810_T|C, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A,
3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6422_T|C, 6725_T|C, 6737_C|T, 6755_C|T, 6938_A|G,
6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 10052_T|C, 10561_T|C
 Case 3 (A.1): KY765322.1




Target: 995 samples       Number of changes: 50                                                 


BC: A.1 + A.1             BC BR: 10-11                  BC BR coord: 2404 - 2405         


Direction L1: <<          Initial region span: 1-8,11-50Gap history (edge excluded): 8-11


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 4.36e-05                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 8 1.103844 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 11 4.49497 None None None * * *



Target sequence

, 56_G|A, 254_A|G, 810_T|C, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A,
3332_G|A, 3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6422_T|C, 6725_T|C, 6737_C|T, 6755_C|T,
6938_A|G, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 10052_T|C, 10561_T|C
 Case 3 (A.1): OK054473.1




Target: 995 samples       Number of changes: 50                                               


BC: A.1 + A.1             BC BR: 8-9                   BC BR coord: 2404 - 2405        


Direction L1: <<          Initial region span: 1-6,9-50Gap history (edge excluded): 6-9


Alt. candidates: [], []                                                                              


Model 1BP/2BP comparison: 1BP vs 2BP: 4.38e-05                                                       


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                          


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 0.760176 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 9 4.965631 None None None * * *



Target sequence

, 254_A|G, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3517_G|A,
3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4373_C|T, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6725_T|C, 6737_C|T, 6755_C|T, 6938_A|G,
6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 9410_C|T, 10052_T|C, 10561_T|C
 Case 3 (A.1): MF801407.1




Target: 995 samples        Number of changes: 44                                               


BC: A.1.NmC1 + A.1         BC BR: 3-4                   BC BR coord: 427 - 428          


Direction L1: <<           Initial region span: 1-3,5-44Gap history (edge excluded): 3-5


Alt. candidates: [], []                                                                               


Model 1BP/2BP comparison:  -                                                                          


Rec. model vs L1: 6.42e-226Rec. model vs L2: 2.87e+04                                          


Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 3 -8.113528 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 5 4.068162 None None None * * *



Target sequence

, 81_T|G, 254_A|G, 272_A|G, 1616_C|T, 1667_C|T, 2030_T|G, 2049_T|C, 2375_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3200_A|G, 3218_T|A, 3247_A|T, 3332_G|A,
3401_C|T, 3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3874_C|T, 4460_T|A, 4784_G|A, 5937_T|C, 6327_A|C, 6377_A|G, 6514_T|C, 6725_T|C, 6737_C|T, 6983_A|G, 7307_T|C, 7451_A|C, 7633_T|C, 7805_T|C,
8045_T|C, 9240_C|T, 9305_C|T, 9353_T|C, 10541_C|T, 10561_T|C
 Case 3 (A.1): KY606274.1




Target: 995 samples       Number of changes: 51                                                   


BC: A.1 + A.1             BC BR: 23-24                   BC BR coord: 3730 - 3731          


Direction L1: <<          Initial region span: 1-22,25-51Gap history (edge excluded): 22-25


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 7.97e-02                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 22 0.805639 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 25 4.472903 None None None * * *



Target sequence

, 71_GG|AC, 732_G|A, 967_C|A, 1615_TC|AG, 1765_G|C, 1865_T|C, 1971_T|G, 2375_C|T, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3308_T|C, 3332_G|A, 3365_A|G, 3502_G|A,
3534_G|A, 3617_G|A, 3674_T|C, 3722_T|C, 3731_C|T, 3863_G|A, 4784_G|A, 5195_G|A, 5315_A|G, 5629_.|C, 5632, 5780_GAC|CTG, 5937_T|C, 6259_T|C, 6327_A|C, 6346_C|T, 6461_A|G, 6725_T|C, 6737_C|T,
6857_C|T, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 8446_G|A, 8636_C|T, 9240_C|T, 9305_C|T, 9353_T|C, 10080_T|A, 10082_GAT|ACA, 10554
 Case 3 (A.1): OK054396.1




Target: 995 samples       Number of changes: 50                                               


BC: A.1 + A.1             BC BR: 8-9                   BC BR coord: 2404 - 2405        


Direction L1: <<          Initial region span: 1-6,9-50Gap history (edge excluded): 6-9


Alt. candidates: [], []                                                                              


Model 1BP/2BP comparison: 1BP vs 2BP: 4.38e-05                                                       


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                          


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 0.760176 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 9 4.965631 None None None * * *



Target sequence

, 254_A|G, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3517_G|A,
3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4373_C|T, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6725_T|C, 6737_C|T, 6755_C|T, 6938_A|G,
6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 9410_C|T, 10052_T|C, 10561_T|C
 Case 3 (A.1): PP431235.1




Target: 995 samples          Number of changes: 41                                                               


BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 23-24, 38-39                 BC BR coord: 3898 - 3899, 10163 - 10164  


Direction L1: >>             Initial region span: 1-9,29-38,39-41Gap history (edge excluded): 9-39 -> 9-29


Alt. candidates: [], []                                                                                                 


Model 1BP/2BP comparison:    2BP vs 1BP: 1.37e-22                                                                       


Rec. model vs L1: 1.51e-34   Rec. model vs L2: 4.23e-07                                                          


Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 9 11.98615 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 29 0.761912 NaN NaN NaN * * *
A.1.NmC2 83 39 0.000000 -51.111068 202.222136 1.365980e-22
A.1.NmC1 181 39 -1.668203 -122.297170 344.594340 1.660319e-53
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 39 3.594399 None None None * * *



Target sequence

, 254_A|G, 428_T|A, 575_T|C, 755_T|C, 875_C|T, 881_G|T, 902_T|G, 1398_C|T, 1616_C|T, 1952_A|G, 2375_C|T, 2534_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A,
3332_G|A, 3459_C|T, 3534_G|A, 3731_C|T, 3902_C|T, 3989_T|C, 4562_C|T, 5937_T|C, 6008_C|T, 6704_G|A, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 7925_C|T, 8051_T|C, 9305_C|T, 9353_T|C, 9800_C|T,
10164_A|G, 10378_A|G, 10561_T|C
 Case 3 (A.1): MF801404.1




Target: 995 samples       Number of changes: 42                                                   


BC: A.1 + A.1             BC BR: 12-13                   BC BR coord: 3730 - 3731          


Direction L1: <<          Initial region span: 1-12,15-42Gap history (edge excluded): 12-15


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 4.24e-02                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 12 0.646224 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 15 3.793318 None None None * * *



Target sequence

, 227_T|A, 254_A|G, 500_A|G, 1816_C|A, 2375_C|T, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3534_G|A, 3554_T|C, 3617_G|A, 3731_C|T, 3788_G|A, 3863_G|A, 4130_A|G, 4576_C|A, 4651_T|C, 4784_G|A,
5102_T|C, 5108_C|A, 5111_C|A, 5117_G|A, 5119_G|A, 5123_G|A, 5195_G|A, 5315_A|G, 5937_T|C, 6327_A|C, 6401_C|T, 6404_C|T, 6725_T|C, 6737_C|T, 6983_A|G, 7633_T|C, 7805_T|C, 9240_C|T, 9305_C|T,
9353_T|C, 10163_T|C, 10340_C|T, 10561_T|C
 Case 3 (A.1): KY765318.1




Target: 995 samples       Number of changes: 49                                                 


BC: A.1 + A.1             BC BR: 9-10                   BC BR coord: 2404 - 2405         


Direction L1: <<          Initial region span: 1-7,10-49Gap history (edge excluded): 7-10


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 4.36e-05                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 7 0.961604 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 10 4.441861 None None None * * *



Target sequence

, 254_A|G, 810_T|C, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A,
3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4154_A|G, 4160_T|C, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6725_T|C, 6737_C|T, 6755_C|T, 6938_A|G,
6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 10052_T|C, 10561_T|C
 Case 3 (A.1): KY765321.1




Target: 995 samples       Number of changes: 49                                                 


BC: A.1 + A.1             BC BR: 8-9                    BC BR coord: 1990 - 1991         


Direction L1: <<          Initial region span: 1-8,11-49Gap history (edge excluded): 8-11


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 1.19e-04                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 8 1.103844 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 11 4.539923 None None None * * *



Target sequence

, 56_G|A, 254_A|G, 810_T|C, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A,
3332_G|A, 3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4154_A|G, 4160_T|C, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6725_T|C, 6737_C|T, 6755_C|T,
6938_A|G, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 10052_T|C
 Case 3 (A.1): OK054469.1




Target: 995 samples       Number of changes: 49                                                 


BC: A.1 + A.1             BC BR: 9-10                   BC BR coord: 2404 - 2405         


Direction L1: <<          Initial region span: 1-7,10-49Gap history (edge excluded): 7-10


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 4.36e-05                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 7 0.961604 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 10 4.441861 None None None * * *



Target sequence

, 254_A|G, 810_T|C, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A,
3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4154_A|G, 4160_T|C, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6725_T|C, 6737_C|T, 6755_C|T, 6938_A|G,
6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 10052_T|C, 10561_T|C
 Case 3 (A.1): KY693679.1




Target: 995 samples        Number of changes: 52                                                 


BC: A.1.NmC2 + A.1         BC BR: 8-9                    BC BR coord: 1405 - 1406         


Direction L1: >>           Initial region span: 1-5,35-52Gap history (edge excluded): 5-35


Alt. candidates: [], []                                                                                 


Model 1BP/2BP comparison:  -                                                                            


Rec. model vs L1: 1.13e-108Rec. model vs L2: 1.23e+00                                            


Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 5 9.392444 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 35 0.495823 None None None * * *



Target sequence

, 254_A|G, 428_T|A, 755_T|C, 875_C|T, 881_G|T, 902_T|G, 980_C|T, 1398_C|T, 1421_C|T, 1592_T|C, 1616_C|T, 2375_C|T, 2534_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A,
3218_T|A, 3332_G|A, 3338_T|C, 3459_C|T, 3534_G|A, 3646_T|C, 3731_C|T, 3902_C|T, 3989_T|C, 4448_T|C, 4547_C|A, 5495_T|C, 5888_T|C, 5937_T|C, 6008_C|T, 6179_C|T, 6422_T|C, 6429_C|T, 6542_C|T,
6983_A|G, 7310_G|A, 7451_A|C, 7633_T|C, 7805_T|C, 8069_T|C, 8621_G|A, 8717_T|C, 9305_C|T, 9353_T|C, 10164_A|G, 10382_A|T, 10384_C|T, 10561_T|C
 Case 3 (A.1): OK054465.1




Target: 995 samples       Number of changes: 51                                                 


BC: A.1 + A.1             BC BR: 9-10                   BC BR coord: 2404 - 2405         


Direction L1: <<          Initial region span: 1-7,10-51Gap history (edge excluded): 7-10


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 4.36e-05                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 7 0.961604 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 10 4.965631 None None None * * *



Target sequence

, 254_A|G, 810_T|C, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A,
3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6725_T|C, 6737_C|T, 6755_C|T, 6914_C|T, 6938_A|G,
6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 8903_A|T, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 10052_T|C, 10561_T|C, 10617_C|T
 Case 3 (A.1): OK054399.1




Target: 995 samples       Number of changes: 46                                               


BC: A.1 + A.1             BC BR: 6-7                   BC BR coord: 1990 - 1991        


Direction L1: <<          Initial region span: 1-6,9-46Gap history (edge excluded): 6-9


Alt. candidates: [], []                                                                              


Model 1BP/2BP comparison: 1BP vs 2BP: 1.19e-04                                                       


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                          


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 0.749621 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 9 4.062776 None None None * * *



Target sequence

, 254_A|G, 810_T|C, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A,
3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6327_A|C, 6725_T|C, 6737_C|T, 6755_C|T, 6938_A|G, 6983_A|G, 7451_A|C, 7633_T|C,
7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 10052_T|C, 10561_T|C
 Case 3 (A.1): OK054466.1




Target: 995 samples       Number of changes: 47                                               


BC: A.1 + A.1             BC BR: 7-8                   BC BR coord: 2404 - 2405        


Direction L1: <<          Initial region span: 1-5,8-47Gap history (edge excluded): 5-8


Alt. candidates: [], []                                                                              


Model 1BP/2BP comparison: 1BP vs 2BP: 4.38e-05                                                       


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                          


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 5 0.549382 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 8 4.441861 None None None * * *



Target sequence

, 254_A|G, 810_T|C, 1380_C|T, 1616_C|T, 1655_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3617_G|A,
3731_C|T, 3863_G|A, 3918_C|T, 4154_A|G, 4160_T|C, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6725_T|C, 6737_C|T, 6755_C|T, 6938_A|G, 6983_A|G, 7451_A|C,
7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 10052_T|C, 10561_T|C
 Case 3 (A.1): MW122387.1




Target: 995 samples       Number of changes: 51                                                   


BC: A.1 + A.1             BC BR: 45-46                   BC BR coord: 9202 - 9203          


Direction L1: >>          Initial region span: 1-44,47-51Gap history (edge excluded): 44-47


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 3.10e-05                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 44 3.802391 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 47 0.315947 None None None * * *



Target sequence

, 254_A|G, 346_T|C, 779_T|C, 1187_G|T, 1412_C|T, 1475_G|A, 1499_A|G, 1616_C|T, 1904_C|T, 2375_C|T, 2426_T|C, 2627_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A,
3332_G|A, 3534_G|A, 3566_T|C, 3593_T|C, 3700_G|A, 3731_C|T, 4883_C|T, 5087_T|C, 5156_T|C, 5315_A|G, 5444_C|T, 5450_T|C, 5651_C|T, 5937_T|C, 5956_T|A, 6503_G|A, 6536_C|T, 6671_T|C, 6983_A|G,
7451_A|C, 7505_C|T, 7633_T|C, 8467_T|C, 8651_C|T, 8852_T|C, 9017_T|C, 9203_A|G, 9242_C|T, 9296_C|T, 9305_C|T, 9353_T|C, 9632_T|C
 Case 3 (A.1): OK054445.1




Target: 995 samples       Number of changes: 47                                                   


BC: A.1 + A.1             BC BR: 41-42                   BC BR coord: 8006 - 8007          


Direction L1: >>          Initial region span: 1-37,42-47Gap history (edge excluded): 37-42


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 2.28e-06                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 37 4.168624 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 42 0.913946 None None None * * *



Target sequence

, 254_A|G, 424_C|T, 1100_C|T, 1616_C|T, 1706_A|G, 2375_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A,
4157_C|T, 4751_T|C, 4784_G|A, 5195_G|A, 5315_A|G, 5342_T|C, 5774_C|T, 5937_T|C, 6236_T|C, 6327_A|C, 6383_C|A, 6419_T|C, 6431_G|A, 6725_T|C, 6737_C|T, 6764_T|C, 6983_A|G, 7226_A|G, 7451_A|C,
7633_T|C, 7652_C|T, 7805_T|C, 8600_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 10040_A|G, 10202_A|G
 Case 3 (A.1): OK054487.1




Target: 995 samples       Number of changes: 48                                                 


BC: A.1 + A.1             BC BR: 9-10                   BC BR coord: 2404 - 2405         


Direction L1: <<          Initial region span: 1-7,10-48Gap history (edge excluded): 7-10


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 4.36e-05                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 7 0.961604 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 10 4.25964 None None None * * *



Target sequence

, 254_A|G, 810_T|C, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A,
3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6725_T|C, 6737_C|T, 6755_C|T, 6938_A|G, 6983_A|G,
7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 10052_T|C, 10561_T|C
 Case 3 (A.1): MF098767.1




Target: 995 samples       Number of changes: 39                                                   


BC: A.1 + A.1             BC BR: 19-20                   BC BR coord: 3988 - 3989          


Direction L1: <<          Initial region span: 1-12,20-39Gap history (edge excluded): 12-20


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 7.62e-06                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 12 1.010384 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 20 3.055187 None None None * * *



Target sequence

, 254_A|G, 1616_C|T, 1919_C|T, 2279_T|A, 2450_A|G, 2681_G|A, 2717_C|T, 2724_T|C, 2925_G|A, 3055_A|G, 3059_G|A, 3071_A|G, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3594_C|T, 3731_C|T, 3917_C|T,
4922_A|T, 5423_A|G, 5937_T|C, 6011_A|G, 6092_C|T, 6561_C|A, 6908_T|C, 7451_A|C, 7481_C|T, 7633_T|C, 7707_G|T, 7805_T|C, 8045_T|C, 8297_A|G, 8606_C|T, 9120_C|T, 9287_C|T, 9305_C|T, 9353_T|C,
9355_G|A
 Case 3 (A.1): OK054391.1




Target: 995 samples       Number of changes: 45                                                 


BC: A.1 + A.1             BC BR: 4-5                    BC BR coord: 1990 - 1991         


Direction L1: <<          Initial region span: 1-3,11-45Gap history (edge excluded): 3-11


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 1.35e-04                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 3 0.451598 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 11 1.727605 None None None * * *



Target sequence

, 254_A|G, 740_G|T, 1439_T|C, 1616_C|T, 2192_C|T, 2375_C|T, 2426_T|C, 2648_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3143_C|T, 3186_G|A, 3218_T|A, 3332_G|A, 3527_A|G,
3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 4287_G|A, 4784_G|A, 4949_G|A, 5195_G|A, 5315_A|G, 5675_T|C, 5937_T|C, 6327_A|C, 6725_T|C, 6737_C|T, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 7851_C|T,
9240_C|T, 9305_C|T, 9353_T|C, 10561_T|C, 10695_A|G, 10703_T|A, 10725_A|G
 Case 3 (A.1): OK054424.1




Target: 995 samples       Number of changes: 50                                                 


BC: A.1 + A.1             BC BR: 10-11                  BC BR coord: 2404 - 2405         


Direction L1: <<          Initial region span: 1-8,11-50Gap history (edge excluded): 8-11


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 2.23e-04                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 8 0.943154 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 11 4.243656 None None None * * *



Target sequence

, 254_A|G, 491_T|C, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2190_A|C, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A,
3332_G|A, 3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6185_T|C, 6327_A|C, 6725_T|C, 6737_C|T, 6755_C|T,
6938_A|G, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 10052_T|C, 10561_T|C
 Case 3 (A.1): OK054448.1




Target: 995 samples       Number of changes: 39                                               


BC: A.1 + A.1             BC BR: 4-5                   BC BR coord: 1990 - 1991        


Direction L1: <<          Initial region span: 1-4,7-39Gap history (edge excluded): 4-7


Alt. candidates: [], []                                                                              


Model 1BP/2BP comparison: 1BP vs 2BP: 1.19e-04                                                       


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                          


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 4 0.330881 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 7 2.895257 None None None * * *



Target sequence

, 254_A|G, 1514_C|T, 1616_C|T, 1655_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3617_G|A, 3731_C|T,
3863_G|A, 3918_C|T, 4160_T|C, 4784_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6327_A|C, 6725_T|C, 6737_C|T, 6983_A|G, 7451_A|C, 7464_A|G, 7633_T|C, 7805_T|C, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C,
10561_T|C
 Case 3 (A.1): OK054410.1




Target: 995 samples       Number of changes: 44                                                   


BC: A.1 + A.1             BC BR: 37-38                   BC BR coord: 8006 - 8007          


Direction L1: >>          Initial region span: 1-33,38-44Gap history (edge excluded): 33-38


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 6.24e-06                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 33 3.51945 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 38 1.183426 None None None * * *



Target sequence

, 1616_C|T, 1706_A|G, 2375_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 4751_T|C, 4784_G|A, 5195_G|A,
5315_A|G, 5342_T|C, 5937_T|C, 6236_T|C, 6327_A|C, 6383_C|A, 6419_T|C, 6431_G|A, 6725_T|C, 6732_G|C, 6737_C|T, 6764_T|C, 6983_A|G, 7226_A|G, 7451_A|C, 7633_T|C, 7652_C|T, 7805_T|C, 8434_A|G,
9240_C|T, 9353_T|C, 9475_G|A, 10040_A|G, 10202_A|G, 10561_T|C
 Case 3 (A.1): OK054404.1




Target: 995 samples       Number of changes: 50                                               


BC: A.1 + A.1             BC BR: 8-9                   BC BR coord: 2404 - 2405        


Direction L1: <<          Initial region span: 1-6,9-50Gap history (edge excluded): 6-9


Alt. candidates: [], []                                                                              


Model 1BP/2BP comparison: 1BP vs 2BP: 4.38e-05                                                       


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                          


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 0.760176 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 9 4.965631 None None None * * *



Target sequence

, 254_A|G, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3517_G|A,
3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4373_C|T, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6725_T|C, 6737_C|T, 6755_C|T, 6938_A|G,
6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 9410_C|T, 10052_T|C, 10561_T|C
 Case 3 (A.1): OK054429.1




Target: 995 samples       Number of changes: 52                                                 


BC: A.1 + A.1             BC BR: 10-11                  BC BR coord: 2404 - 2405         


Direction L1: <<          Initial region span: 1-8,11-52Gap history (edge excluded): 8-11


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 4.36e-05                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 8 1.196935 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 11 4.816652 None None None * * *



Target sequence

, 254_A|G, 810_T|C, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 1941_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A,
3332_G|A, 3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6662_G|A, 6725_T|C, 6737_C|T, 6755_C|T,
6872_C|T, 6938_A|G, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 9518_A|G, 10052_T|C, 10561_T|C
 Case 3 (A.1): OK054452.1




Target: 995 samples       Number of changes: 51                                               


BC: A.1 + A.1             BC BR: 8-9                   BC BR coord: 2404 - 2405        


Direction L1: <<          Initial region span: 1-6,9-51Gap history (edge excluded): 6-9


Alt. candidates: [], []                                                                              


Model 1BP/2BP comparison: 1BP vs 2BP: 4.38e-05                                                       


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                          


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 0.760176 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 9 5.200961 None None None * * *



Target sequence

, 254_A|G, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3517_G|A,
3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4373_C|T, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6350_G|A, 6725_T|C, 6737_C|T, 6755_C|T,
6938_A|G, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 9410_C|T, 10052_T|C, 10561_T|C
 Case 3 (A.1): OK054386.1




Target: 995 samples       Number of changes: 46                                                   


BC: A.1 + A.1             BC BR: 38-39                   BC BR coord: 7516 - 7517          


Direction L1: >>          Initial region span: 1-33,41-46Gap history (edge excluded): 33-41


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 5.15e-13                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 33 3.87673 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 41 0.678615 None None None * * *



Target sequence

, 254_A|G, 431_T|C, 512_C|T, 1616_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 4157_C|T,
4286_C|T, 4784_G|A, 5195_G|A, 5315_A|G, 5937_T|C, 6071_C|T, 6327_A|C, 6383_C|A, 6419_T|C, 6431_G|A, 6537_A|G, 6678_T|C, 6725_T|C, 6737_C|T, 6764_T|C, 6983_A|G, 6987_A|G, 7224_T|C, 7451_A|C,
7633_T|C, 7805_T|C, 8258_A|G, 9240_C|T, 9305_C|T, 9353_T|C, 10040_A|G, 10751_G|A
 Case 3 (A.1): OK054394.1




Target: 995 samples       Number of changes: 38                                                 


BC: A.1 + A.1             BC BR: 6-7                    BC BR coord: 2798 - 2799         


Direction L1: <<          Initial region span: 1-6,15-38Gap history (edge excluded): 6-15


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 1.31e-09                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 0.348379 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 15 3.185527 None None None * * *



Target sequence

, 882_T|G, 1616_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3254_T|C, 3332_G|A, 3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 4236_A|G, 4592_A|G,
4784_G|A, 5139_G|A, 5195_G|A, 5315_A|G, 5937_T|C, 6327_A|C, 6461_A|G, 6725_T|C, 6737_C|T, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 8375_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 10561_T|C, 10702_A|C
 Case 3 (A.1): OK054443.1




Target: 995 samples       Number of changes: 49                                               


BC: A.1 + A.1             BC BR: 5-6                   BC BR coord: 1990 - 1991        


Direction L1: <<          Initial region span: 1-5,8-49Gap history (edge excluded): 5-8


Alt. candidates: [], []                                                                              


Model 1BP/2BP comparison: 1BP vs 2BP: 1.19e-04                                                       


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                          


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 5 0.7983 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 8 4.965631 None None None * * *



Target sequence

, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3517_G|A, 3534_G|A,
3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4373_C|T, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6725_T|C, 6737_C|T, 6755_C|T, 6938_A|G, 6983_A|G,
7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 9410_C|T, 10052_T|C, 10561_T|C
 Case 3 (A.1): OK054480.1




Target: 995 samples       Number of changes: 51                                               


BC: A.1 + A.1             BC BR: 8-9                   BC BR coord: 2404 - 2405        


Direction L1: <<          Initial region span: 1-6,9-51Gap history (edge excluded): 6-9


Alt. candidates: [], []                                                                              


Model 1BP/2BP comparison: 1BP vs 2BP: 4.38e-05                                                       


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                          


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 0.760176 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 9 5.200961 None None None * * *



Target sequence

, 254_A|G, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3517_G|A,
3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4373_C|T, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6350_G|A, 6725_T|C, 6737_C|T, 6755_C|T,
6938_A|G, 6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 9410_C|T, 10052_T|C, 10561_T|C
 Case 3 (A.1): MK269353.1




Target: 995 samples       Number of changes: 48                                                   


BC: A.1 + A.1             BC BR: 39-40                   BC BR coord: 7516 - 7517          


Direction L1: >>          Initial region span: 1-39,46-48Gap history (edge excluded): 39-46


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 2.27e-02                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 39 3.740661 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 46 0.705991 None None None * * *



Target sequence

, 254_A|G, 374_T|C, 725_A|G, 1616_C|T, 1706_A|G, 2375_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A,
4571_T|C, 4784_G|A, 5033_A|G, 5195_G|A, 5315_A|G, 5937_T|C, 6014_T|C, 6327_A|C, 6383_C|A, 6419_T|C, 6431_G|A, 6725_T|C, 6737_C|T, 6764_T|C, 6965_G|A, 6983_A|G, 7271_C|T, 7375_T|C, 7451_A|C,
7463_C|T, 7633_T|C, 7805_T|C, 8360_A|G, 9305_C|T, 9353_T|C, 9366_T|C, 9464_C|T, 10040_A|G, 10300_10302
 Case 3 (A.1): MF434522.1




Target: 995 samples       Number of changes: 50                                                 


BC: A.1 + A.1             BC BR: 7-8                    BC BR coord: 1990 - 1991         


Direction L1: <<          Initial region span: 1-5,14-50Gap history (edge excluded): 5-14


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 3.21e-08                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 5 0.770223 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 14 4.181436 None None None * * *



Target sequence

, 254_A|G, 722_C|T, 1180_T|C, 1298_T|C, 1328_T|C, 1616_C|T, 1865_T|C, 2372_A|G, 2375_C|T, 2388_T|C, 2654_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2879_T|C, 2925_G|A, 3030_C|T, 3059_G|A, 3140_A|G,
3186_G|A, 3218_T|A, 3221_C|T, 3332_G|A, 3338_T|C, 3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 4014_G|A, 4076_C|T, 4784_G|A, 5195_G|A, 5315_A|G, 5937_T|C, 6327_A|C, 6461_A|G, 6725_T|C, 6737_C|T,
6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 7898_C|T, 8246_A|G, 8762_A|G, 9240_C|T, 9305_C|T, 9353_T|C, 10390_T|C, 10561_T|C
 Case 3 (A.1): KY272987.1




Target: 995 samples        Number of changes: 162                                                     


BC: A.1 + A.1.NmC1         BC BR: 156-157                   BC BR coord: 10288 - 10289         


Direction L1: <<           Initial region span: 1-79,159-162Gap history (edge excluded): 79-159


Alt. candidates: [], []                                                                                      


Model 1BP/2BP comparison:  -                                                                                 


Rec. model vs L1: 1.49e+09 Rec. model vs L2: 0.00e+00                                                 


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 79 0.857624 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 159 1.925944 NaN NaN NaN * * *
A.1 995 101 1.598220 -1.41091 16.821819 37049.124492 *



Target sequence

, 254_A|G, 407_G|A, 423_G|A, 428_T|C, 467_T|C, 523_A|G, 558_T|C, 653_G|A, 719_T|C, 737_A|G, 773_T|C, 803_A|G, 884_A|G, 974_C|T, 1046_T|C, 1139_G|A, 1175_A|G, 1328_T|C, 1391_G|A, 1520_G|A,
1616_C|T, 1718_C|T, 1748_T|C, 1763_A|G, 1781_C|T, 1875_T|C, 1896_T|C, 1922_C|T, 2066_C|T, 2309_C|T, 2375_C|T, 2411_C|T, 2436_A|G, 2471_A|G, 2519_G|A, 2522_G|A, 2525_G|A, 2576_G|A, 2606_C|T,
2648_T|G, 2681_G|A, 2724_T|C, 2846_G|A, 2925_G|A, 2969_C|T, 3008_A|G, 3014_T|C, 3038_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3266_C|T, 3332_G|A,
3340_A|G, 3534_G|A, 3587_T|C, 3615_C|T, 3697_T|C, 3731_C|T, 3869_CT|TC, 3885_T|C, 3893_T|A, 3977_T|C, 3989_T|C, 3992_C|T, 4031_C|T, 4085_T|C, 4106_A|G, 4145_C|T, 4238_C|T, 4244_A|G, 4295_A|G,
4403_A|G, 4445_C|T, 4454_G|T, 4493_C|T, 4523_G|A, 4595_C|T, 4733_T|C, 4817_C|T, 4943_G|A, 4961_T|C, 5000_T|C, 5003_C|T, 5060_T|C, 5153_G|A, 5210_G|A, 5282_T|C, 5369_C|T, 5375_A|G, 5387_C|T,
5405_C|T, 5546_T|C, 5591_T|C, 5744_A|G, 5828_T|C, 5937_T|C, 6101_T|C, 6119_C|T, 6155_A|G, 6164_C|T, 6230_A|G, 6233_T|C, 6275_A|T, 6473_T|A, 6635_T|C, 6645_C|T, 6684_A|C, 6807_T|C, 6851_C|T,
6890_A|G, 6911_C|T, 6935_G|A, 6938_A|G, 6983_A|G, 7037_C|T, 7043_T|C, 7049_CT|TC, 7079_A|G, 7364_T|C, 7451_A|C, 7517_C|T, 7633_T|C, 7796_C|T, 7805_T|C, 7808_T|C, 7964_A|G, 8007_G|A, 8105_C|T,
8177_T|C, 8408_T|C, 8516_A|G, 8606_C|T, 8787_G|A, 9017_T|C, 9110_G|A, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9464_C|T, 9503_C|T, 9527_A|G, 9671_T|A, 9797_T|C, 9848_G|C, 9881_C|T, 9935_A|G,
10052_T|C, 10127_T|C, 10275_A|C, 10361_T|C, 10376_G|A, 10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): MW122443.1




Target: 995 samples       Number of changes: 55                                                   


BC: A.1 + A.1             BC BR: 25-26                   BC BR coord: 3898 - 3899          


Direction L1: <<          Initial region span: 1-24,29-55Gap history (edge excluded): 24-29


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 2.82e-12                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 24 2.335119 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 29 3.252077 None None None * * *



Target sequence

, 254_A|G, 346_T|C, 398_T|C, 779_T|C, 1187_G|T, 1228_A|G, 1475_G|A, 1499_A|G, 1616_C|T, 1904_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2855_C|T, 2925_G|A, 3041_T|C, 3059_G|A, 3140_A|G, 3186_G|A,
3218_T|A, 3332_G|A, 3534_G|A, 3566_T|C, 3593_T|C, 3731_C|T, 4457_A|G, 4502_C|T, 4520_C|T, 4883_C|T, 5087_T|C, 5156_T|C, 5315_A|G, 5937_T|C, 6167_T|A, 6629_T|A, 6659_G|A, 6671_T|C, 6983_A|G,
7010_T|A, 7094_T|C, 7151_T|C, 7451_A|C, 7505_C|T, 7633_T|C, 7748_C|T, 7805_T|C, 8852_T|C, 9017_T|C, 9242_C|T, 9305_C|T, 9335_C|T, 9353_T|C, 9591_T|C, 9918_C|A, 10262_T|C
 Case 3 (A.1): KX922708.1




Target: 995 samples       Number of changes: 52                                                   


BC: A.1 + A.1             BC BR: 14-15                   BC BR coord: 3031 - 3032          


Direction L1: <<          Initial region span: 1-14,27-52Gap history (edge excluded): 14-27


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 9.16e-04                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 14 1.646494 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 27 3.792913 None None None * * *



Target sequence

, 254_A|G, 506_T|C, 1571_T|C, 1616_C|T, 2060_T|C, 2408_G|A, 2435_T|C, 2460_T|C, 2681_G|A, 2717_C|T, 2724_T|C, 2861_C|T, 2925_G|A, 2978_T|C, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A,
3722_T|C, 3731_C|T, 4166_G|A, 5198_T|C, 5249_C|T, 5369_C|T, 5636_A|G, 5840_T|C, 5937_T|C, 6149_C|T, 6278_C|T, 6908_T|C, 7451_A|C, 7601_A|G, 7633_T|C, 7805_T|C, 8006_C|T, 8045_T|C, 8250_C|T,
8258_A|G, 8606_C|T, 8621_G|A, 8631_A|G, 8852_T|C, 9287_C|T, 9305_C|T, 9311_G|A, 9353_T|C, 9395_C|T, 10090_C|T, 10301_T|G, 10340_C|T, 10561_T|C
 Case 3 (A.1): OK054425.1




Target: 995 samples       Number of changes: 48                                                 


BC: A.1 + A.1             BC BR: 9-10                   BC BR coord: 2404 - 2405         


Direction L1: <<          Initial region span: 1-7,10-48Gap history (edge excluded): 7-10


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 4.36e-05                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 7 0.961604 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 10 4.25964 None None None * * *



Target sequence

, 254_A|G, 810_T|C, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A,
3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6725_T|C, 6737_C|T, 6755_C|T, 6938_A|G, 6983_A|G,
7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 10052_T|C, 10561_T|C
 Case 3 (A.1): OQ661916.1




Target: 995 samples        Number of changes: 167                                                     


BC: A.1 + A.1.NmC1         BC BR: 163-164                   BC BR coord: 10288 - 10289         


Direction L1: <<           Initial region span: 1-53,164-167Gap history (edge excluded): 53-164


Alt. candidates: [], []                                                                                      


Model 1BP/2BP comparison:  -                                                                                 


Rec. model vs L1: 9.87e+00 Rec. model vs L2: 0.00e+00                                                 


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 53 1.034327 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 164 1.925944 NaN NaN NaN * * *
A.1 995 131 1.240166 -1.739254 13.478508 0.171187 *



Target sequence

, 50_A|G, 254_A|G, 346_T|C, 423_G|A, 434_T|C, 467_T|C, 523_A|G, 530_T|C, 558_T|C, 575_T|C, 617_C|T, 653_G|A, 719_T|C, 803_A|G, 884_A|G, 941_C|T, 962_T|C, 1175_A|G, 1193_C|T, 1325_C|T,
1493_T|C, 1616_C|T, 1718_C|T, 1896_T|C, 1922_C|T, 2060_T|A, 2066_C|T, 2132_T|C, 2207_A|G, 2375_C|T, 2394_A|T, 2411_C|T, 2460_T|C, 2492_T|C, 2519_G|A, 2525_G|A, 2576_G|A, 2594_T|C, 2606_C|T,
2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C, 2804_C|T, 2846_G|A, 2925_G|A, 2960_T|C, 2973_G|A, 2978_T|C, 3002_T|C, 3038_T|C, 3059_G|A, 3110_T|C, 3131_G|A, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A,
3218_T|A, 3254_T|C, 3266_C|T, 3308_T|C, 3332_G|A, 3344_C|T, 3518_C|T, 3534_G|A, 3731_C|T, 3885_T|C, 3989_T|C, 4052_G|A, 4085_T|C, 4238_C|T, 4241_A|G, 4295_A|G, 4409_A|T, 4454_G|A, 4493_C|T,
4523_G|A, 4652_A|G, 4733_T|C, 4850_C|T, 4889_C|T, 4914_C|G, 4952_C|T, 5000_T|C, 5060_T|C, 5177_G|A, 5198_T|C, 5238_G|A, 5267_T|C, 5369_C|T, 5375_A|G, 5387_C|T, 5501_A|G, 5546_T|C, 5591_T|C,
5639_G|A, 5744_A|G, 5828_T|C, 5906_G|A, 5937_T|C, 5987_G|T, 6056_C|T, 6101_T|C, 6155_A|G, 6164_C|T, 6179_C|T, 6251_C|A, 6275_A|C, 6363_C|T, 6473_T|A, 6684_A|C, 6807_T|C, 6827_T|C, 6890_A|G,
6911_C|T, 6983_A|G, 7037_C|T, 7050_T|C, 7064_T|C, 7079_A|G, 7176_G|A, 7331_G|A, 7358_T|C, 7367_A|G, 7451_A|C, 7496_G|A, 7506_C|T, 7517_C|T, 7633_T|C, 7637_A|G, 7739_C|T, 7805_T|C, 7898_C|T,
8006_CG|TA, 8408_T|C, 8516_A|G, 8606_C|T, 8651_C|T, 8753_T|A, 8804_T|C, 9017_T|C, 9098_T|C, 9206_A|G, 9222_G|A, 9303_T|C, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9473_G|A, 9503_C|T, 9509_T|C,
9527_A|G, 9582_C|T, 9591_T|C, 9620_C|T, 9623_C|T, 9746_A|G, 9806_C|T, 9926_T|C, 10161_G|A, 10262_T|C, 10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): OK054403.1




Target: 995 samples       Number of changes: 50                                               


BC: A.1 + A.1             BC BR: 5-6                   BC BR coord: 1990 - 1991        


Direction L1: <<          Initial region span: 1-5,8-50Gap history (edge excluded): 5-8


Alt. candidates: [], []                                                                              


Model 1BP/2BP comparison: 1BP vs 2BP: 1.19e-04                                                       


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                          


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 5 0.7983 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 8 5.200961 None None None * * *



Target sequence

, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 1904_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3517_G|A, 3534_G|A,
3617_G|A, 3731_C|T, 3863_G|A, 3918_C|T, 4160_T|C, 4373_C|T, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6350_G|A, 6725_T|C, 6737_C|T, 6755_C|T, 6938_A|G,
6983_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 9125_G|A, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 9410_C|T, 10052_T|C, 10561_T|C
 Case 3 (A.1): MW122429.1




Target: 995 samples       Number of changes: 50                                                   


BC: A.1 + A.1             BC BR: 25-26                   BC BR coord: 3898 - 3899          


Direction L1: <<          Initial region span: 1-22,26-50Gap history (edge excluded): 22-26


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 3.13e-01                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 22 1.171311 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 26 2.878853 None None None * * *



Target sequence

, 254_A|G, 346_T|C, 662_T|C, 779_T|C, 1187_G|T, 1475_G|A, 1499_A|G, 1616_C|T, 1904_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2855_C|T, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A,
3534_G|A, 3566_T|C, 3593_T|C, 3722_T|C, 3731_C|T, 3821_T|C, 4883_C|T, 5087_T|C, 5156_T|C, 5315_A|G, 5937_T|C, 6007_A|G, 6629_T|A, 6671_T|C, 6920_A|G, 6983_A|G, 7094_T|C, 7151_T|C, 7451_A|C,
7505_C|T, 7633_T|C, 7805_T|C, 7952_C|T, 8852_T|C, 8897_A|G, 9017_T|C, 9242_C|T, 9262_A|T, 9296_C|T, 9305_C|T, 9353_T|C
 Case 3 (A.1): OK054370.1




Target: 995 samples       Number of changes: 38                                               


BC: A.1 + A.1             BC BR: 4-5                   BC BR coord: 1990 - 1991        


Direction L1: <<          Initial region span: 1-4,7-38Gap history (edge excluded): 4-7


Alt. candidates: [], []                                                                              


Model 1BP/2BP comparison: 1BP vs 2BP: 1.19e-04                                                       


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                          


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 4 0.586317 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 7 3.182625 None None None * * *



Target sequence

, 1380_C|T, 1514_C|T, 1616_C|T, 1655_C|T, 2192_C|T, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3617_G|A, 4784_G|A,
5195_G|A, 5315_A|G, 5937_T|C, 6029_G|A, 6152_C|T, 6327_A|C, 6725_T|C, 6737_C|T, 6755_C|T, 6938_A|G, 6983_A|G, 7451_A|C, 7633_T|C, 9211_G|A, 9240_C|T, 9305_C|T, 9353_T|C, 10052_T|C, 10561_T|C
 Case 3 (A.1): PP431245.1




Target: 995 samples          Number of changes: 38                                                                  


BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 22-23, 34-35                  BC BR coord: 3898 - 3899, 9304 - 9305      


Direction L1: >>             Initial region span: 1-18,28-34,35-38Gap history (edge excluded): 18-35 -> 18-28


Alt. candidates: [], []                                                                                                    


Model 1BP/2BP comparison:    2BP vs 1BP: 1.65e-13                                                                          


Rec. model vs L1: 1.21e-22   Rec. model vs L2: 5.01e-06                                                             


Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 18 14.324339 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 28 0.490344 NaN NaN NaN * * *
A.1.NmC1 181 35 0.000000 -72.070200 222.140399 1.859184e-31
A.1.NmC2 83 35 -1.529105 -32.743139 143.486279 2.228194e-14
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 83 35 2.741564 None None None * * *



Target sequence

, 254_A|G, 428_T|A, 755_T|C, 875_C|T, 881_G|T, 902_T|G, 1398_C|T, 1616_C|T, 2375_C|T, 2534_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3350_G|A,
3459_C|T, 3534_G|A, 3731_C|T, 3902_C|T, 3989_T|C, 5267_T|C, 5937_T|C, 6008_C|T, 6233_T|C, 6983_A|G, 7064_T|C, 7451_A|C, 7633_T|C, 7805_T|C, 8390_G|A, 9305_C|T, 9353_T|C, 10164_A|G, 10561_T|C
 Case 3 (A.1): MW915412.1




Target: 995 samples        Number of changes: 79                                                 


BC: A.1 + A.1.NmC1         BC BR: 75-76                  BC BR coord: 10288 - 10289       


Direction L1: >>           Initial region span: 1-5,76-79Gap history (edge excluded): 5-76


Alt. candidates: [], []                                                                                 


Model 1BP/2BP comparison:  -                                                                            


Rec. model vs L1: 1.77e+06 Rec. model vs L2: 3.99e-245                                           


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 5 0.90573 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 76 3.420355 None None None * * *



Target sequence

, 19_A|G, 212_C|T, 233_G|A, 254_A|G, 320_A|G, 523_A|G, 558_T|C, 653_G|A, 716_C|T, 719_T|C, 1175_A|G, 1232_A|G, 1343_C|T, 1398_C|T, 1538_A|G, 1568_C|T, 1616_C|T, 1760_A|G, 1994_C|T, 2375_C|T,
2498_G|A, 2654_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 2936_A|G, 3035_C|T, 3038_T|C, 3059_G|A, 3070_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3248_T|C, 3254_T|C, 3311_A|G, 3455_G|A, 3482_T|C,
3518_C|T, 3534_G|A, 3731_C|T, 3902_C|T, 4085_T|C, 4454_G|A, 4472_T|C, 4499_C|A, 4676_A|C, 4937_C|T, 5000_T|C, 5060_T|C, 5375_A|G, 5564_C|T, 5828_T|C, 5937_T|C, 5975_C|T, 6056_C|T, 6140_A|G,
6254_T|C, 6266_T|C, 6269_C|T, 6308_C|T, 6311_G|A, 6363_C|T, 7451_A|C, 7517_C|T, 7633_T|C, 7805_T|C, 7836_C|A, 8007_G|A, 8045_T|C, 8144_A|T, 8408_T|C, 8477_T|A, 9017_T|C, 10392_A|G, 10477_T|C,
10561_T|C, 10579_A|G
 Case 3 (A.1): MW165880.1




Target: 995 samples       Number of changes: 53                                                   


BC: A.1 + A.1             BC BR: 23-24                   BC BR coord: 3898 - 3899          


Direction L1: <<          Initial region span: 1-22,25-53Gap history (edge excluded): 22-25


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 2.35e-01                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 22 1.626525 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 25 3.848374 None None None * * *



Target sequence

, 185_C|T, 254_A|G, 456_C|T, 497_T|C, 1475_G|A, 1616_C|T, 1904_C|T, 2375_C|T, 2600_C|T, 2621_A|G, 2681_G|A, 2724_T|C, 2925_G|A, 3056_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A,
3534_G|A, 3566_T|C, 3593_T|C, 3731_C|T, 3911_A|G, 4394_T|C, 4982_T|C, 5156_T|C, 5213_A|G, 5315_A|G, 5774_C|T, 5937_T|C, 6599_G|A, 6629_T|A, 6671_T|C, 6776_A|G, 6983_A|G, 7094_T|C, 7379_T|C,
7451_A|C, 7633_T|C, 7805_T|C, 7917_A|C, 8165_C|T, 8474_C|T, 9137_T|C, 9242_C|T, 9296_C|T, 9305_C|T, 9353_T|C, 9824_T|C, 9971_T|C, 10421_C|T, 10561_T|C
 Case 3 (A.1): MW122411.1




Target: 995 samples       Number of changes: 49                                                   


BC: A.1 + A.1             BC BR: 16-17                   BC BR coord: 3136 - 3137          


Direction L1: <<          Initial region span: 1-13,22-49Gap history (edge excluded): 13-22


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 3.98e-06                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 13 1.831311 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 22 3.219804 None None None * * *



Target sequence

, 254_A|G, 346_T|C, 779_T|C, 1187_G|T, 1475_G|A, 1499_A|G, 1616_C|T, 1668_A|G, 1904_C|T, 2298_T|C, 2375_C|T, 2681_G|A, 2855_C|T, 2925_G|A, 3032_A|T, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A,
3332_G|A, 3534_G|A, 3566_T|C, 3593_T|C, 3731_C|T, 4883_C|T, 5087_T|C, 5156_T|C, 5315_A|G, 5937_T|C, 6629_T|A, 6671_T|C, 6983_A|G, 7010_T|A, 7094_T|C, 7151_T|C, 7451_A|C, 7505_C|T, 7633_T|C,
7805_T|C, 8153_C|T, 8510_C|T, 8852_T|C, 9017_T|C, 9242_C|T, 9296_C|T, 9305_C|T, 9353_T|C, 9643_G|A, 10262_T|C
 Case 3 (A.1): KY328290.1




Target: 995 samples       Number of changes: 125                                                   


BC: A.1 + A.1             BC BR: 96-97                    BC BR coord: 7450 - 7451          


Direction L1: <<          Initial region span: 1-6,118-125Gap history (edge excluded): 6-118


Alt. candidates: [], []                                                                                   


Model 1BP/2BP comparison: 1BP vs 2BP: 7.97e-06                                                            


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                               


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 1.053606 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 118 1.558047 None None None * * *



Target sequence

, 159_AA|GG, 212_C|T, 254_A|G, 308_T|C, 423_G|A, 467_T|C, 479_G|A, 523_A|G, 558_T|C, 653_G|A, 719_T|C, 803_A|G, 884_A|G, 1175_A|G, 1616_C|T, 1920_A|T, 1960_T|A, 2066_C|G, 2084_T|A, 2375_C|T,
2411_C|T, 2519_G|A, 2525_G|A, 2576_G|A, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C, 2846_G|A, 2925_G|A, 3038_T|C, 3059_G|A, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C,
3266_C|T, 3332_G|A, 3395_T|A, 3518_C|T, 3534_G|A, 3731_C|T, 3885_T|C, 3989_T|C, 3992_C|T, 4085_T|C, 4106_A|G, 4238_C|T, 4295_A|G, 4454_G|A, 4493_C|T, 4523_G|A, 4595_C|T, 4652_A|G, 4733_T|C,
4790_A|G, 4850_C|T, 4952_C|T, 5000_T|C, 5003_C|T, 5060_T|C, 5091_A|G, 5177_G|A, 5267_T|C, 5333_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5546_T|C, 5591_T|C, 5744_A|G, 5780_G|A, 5828_T|C, 5888_T|C,
5937_T|C, 6056_C|T, 6101_T|C, 6155_A|G, 6164_C|T, 6275_A|T, 6363_C|T, 6473_T|A, 6684_A|C, 6807_T|C, 6890_A|G, 6911_C|T, 6980_G|A, 6983_A|G, 7037_C|T, 7050_T|C, 7079_A|G, 7358_T|C, 7451_AG|CA,
7517_C|T, 7523_T|C, 7633_T|C, 7784_G|A, 7805_T|C, 7826_T|C, 8007_G|A, 8105_C|T, 8165_C|T, 8394_C|G, 8408_T|C, 8516_A|G, 8606_C|T, 8615_G|A, 8631_A|G, 9017_T|C, 9305_C|T, 9353_T|C, 9434_A|G,
9455_G|A, 9500_T|C, 9503_C|T, 9509_T|C, 9527_A|G, 9533_T|C, 9591_T|C, 9884_G|A, 10163_T|A, 10262_T|C
 Case 3 (A.1): MW122412.1




Target: 995 samples       Number of changes: 53                                                   


BC: A.1 + A.1             BC BR: 10-11                   BC BR coord: 1990 - 1991          


Direction L1: <<          Initial region span: 1-10,23-53Gap history (edge excluded): 10-23


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 1.30e-09                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 10 1.241955 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 23 2.997812 None None None * * *



Target sequence

, 254_A|G, 346_T|C, 779_T|C, 1187_G|T, 1196_C|T, 1250_C|T, 1475_G|A, 1499_A|G, 1616_C|T, 1904_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 2975_A|G, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A,
3254_T|C, 3332_G|A, 3534_G|A, 3566_T|C, 3593_T|C, 3731_C|T, 4883_C|T, 5087_T|C, 5156_T|C, 5315_A|G, 5831_C|T, 5936_TT|CC, 6629_T|A, 6671_T|C, 6982_GA|AG, 7094_T|C, 7151_T|C, 7264_T|C,
7313_T|C, 7451_A|C, 7505_C|T, 7633_T|C, 7805_T|C, 8076_G|T, 8477_T|C, 8540_A|G, 8852_T|C, 9017_T|C, 9242_C|T, 9296_C|T, 9305_C|T, 9331_C|T, 9353_T|C, 9977_C|T
 Case 3 (A.1): MW915413.1




Target: 995 samples       Number of changes: 92                                                 


BC: A.1 + A.1             BC BR: 85-86                  BC BR coord: 9439 - 9440         


Direction L1: <<          Initial region span: 1-4,86-92Gap history (edge excluded): 4-86


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 3.27e-11                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 4 0.536868 NaN NaN NaN * * *
A.1.NmC1 181 7 -9.392192 -328.607928 883.215856 1.418114e-139
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 86 1.647312 None None None * * *



Target sequence

, 19_A|G, 233_G|A, 254_A|G, 476_G|A, 523_A|G, 558_T|C, 653_G|A, 716_C|T, 1175_A|G, 1343_C|T, 1398_C|T, 1538_A|G, 1568_C|T, 1616_C|T, 1760_A|G, 1994_C|T, 2375_C|T, 2498_G|A, 2654_C|T,
2681_G|A, 2724_T|C, 2925_G|A, 2936_A|G, 3035_C|T, 3038_T|C, 3059_G|A, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3248_T|C, 3254_T|C, 3311_A|G, 3332_G|A, 3386_A|G, 3455_G|A, 3482_T|C, 3518_C|T,
3534_G|A, 3627_A|G, 3731_C|T, 3902_C|T, 4085_T|C, 4454_G|A, 4472_T|C, 4499_C|A, 4676_A|C, 5000_T|C, 5060_T|C, 5375_A|G, 5564_C|T, 5828_T|C, 5937_T|C, 5975_C|T, 6056_C|T, 6140_A|G, 6254_T|C,
6266_T|C, 6269_C|T, 6308_C|T, 6311_G|A, 6363_C|T, 6629_T|C, 6698_A|G, 6731_G|A, 6797_T|C, 6917_T|C, 6981_G|A, 6983_A|G, 7014_C|T, 7451_A|C, 7457_C|T, 7517_C|T, 7633_T|C, 7805_T|C, 8007_G|A,
8045_T|C, 8144_A|T, 8408_T|C, 8477_T|A, 9017_T|C, 9305_C|T, 9344_G|A, 9353_T|C, 9434_A|G, 9569_A|G, 9596_G|A, 9757_A|G, 9800_C|T, 9866_A|G, 9869_T|C, 10223_C|T
 Case 3 (A.1): MW915414.1




Target: 995 samples        Number of changes: 100                                                 


BC: A.1 + A.1.NmC1         BC BR: 96-97                   BC BR coord: 10288 - 10289       


Direction L1: <<           Initial region span: 1-4,97-100Gap history (edge excluded): 4-97


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison:  -                                                                             


Rec. model vs L1: 6.60e-01 Rec. model vs L2: 3.27e-317                                            


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 4 0.670399 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 97 4.261319 None None None * * *



Target sequence

, 19_A|G, 233_G|A, 254_A|G, 371_G|A, 523_A|G, 558_T|C, 629_A|G, 653_G|A, 716_C|T, 1143_G|A, 1175_A|G, 1286_T|C, 1538_A|G, 1568_C|T, 1616_C|T, 1649_T|A, 1760_A|G, 1901_T|C, 2041_T|C, 2375_C|T,
2654_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 2936_A|G, 3035_C|T, 3059_G|A, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3242_C|T, 3248_T|C, 3311_A|G, 3332_G|A, 3455_G|A, 3482_T|C, 3518_C|T, 3534_G|A,
3709_C|T, 3731_C|T, 3902_C|T, 4085_T|C, 4169_G|A, 4454_G|A, 4472_T|C, 4499_C|A, 4664_G|A, 5000_T|C, 5003_C|T, 5060_T|C, 5375_A|G, 5387_C|T, 5537_C|T, 5540_G|A, 5564_C|T, 5684_A|G, 5813_T|C,
5828_T|C, 5937_T|C, 5975_C|T, 6056_C|T, 6140_A|G, 6248_G|A, 6254_T|C, 6269_C|T, 6308_C|T, 6363_C|T, 6629_T|C, 6698_A|G, 6731_G|A, 6917_T|C, 6981_G|A, 6983_A|G, 7014_C|T, 7281_T|C, 7451_A|C,
7517_C|T, 7633_T|C, 7805_T|C, 8007_G|A, 8045_T|C, 8408_T|C, 8477_T|A, 8702_C|T, 9017_T|C, 9305_C|T, 9344_G|A, 9353_T|C, 9434_A|G, 9569_A|G, 9596_G|A, 9757_A|G, 9866_A|G, 10188_T|C, 10223_C|T,
10364_A|G, 10392_A|G, 10477_T|C, 10561_T|C
 Case 3 (A.1): MH119185.1




Target: 995 samples       Number of changes: 160                                                     


BC: A.1 + A.1.NmC1        BC BR: 154-155                   BC BR coord: 10288 - 10289         


Direction L1: >>          Initial region span: 1-51,158-160Gap history (edge excluded): 51-158


Alt. candidates: [], []                                                                                     


Model 1BP/2BP comparison: 1BP vs 2BP: 3.13e-02                                                              


Rec. model vs L1: 1.88e+14Rec. model vs L2: 0.00e+00                                                 


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 51 1.968418 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 158 1.972602 NaN NaN NaN * * *
A.1 995 145 0.600565 -1.268593 16.537187 1.328857e+08 *



Target sequence

, 212_C|T, 254_A|G, 423_G|A, 467_T|C, 496_G|A, 523_A|G, 558_T|C, 575_T|C, 653_G|A, 719_T|C, 803_A|G, 884_A|G, 1097_T|A, 1160_T|C, 1175_A|G, 1263_T|C, 1325_C|T, 1616_C|T, 1718_C|T, 1777_C|T,
1875_T|C, 1896_T|C, 1922_C|T, 2060_T|A, 2066_C|T, 2132_T|C, 2207_A|G, 2233_A|G, 2375_C|T, 2394_A|T, 2411_C|T, 2460_T|C, 2492_T|C, 2519_G|A, 2525_G|A, 2576_G|A, 2606_C|T, 2648_T|G, 2654_C|T,
2681_G|A, 2724_T|C, 2804_C|T, 2846_G|A, 2925_G|A, 2960_T|C, 2973_G|A, 3002_T|C, 3038_T|C, 3059_G|A, 3110_T|C, 3123_C|T, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3266_C|T,
3290_A|T, 3308_T|C, 3332_G|A, 3344_C|T, 3500_C|T, 3518_C|T, 3534_G|A, 3731_C|T, 3885_T|C, 3917_C|A, 3989_T|C, 4085_T|C, 4238_C|T, 4295_A|G, 4415_T|C, 4454_G|A, 4493_C|T, 4523_G|A, 4595_C|T,
4607_A|G, 4652_A|G, 4733_T|C, 4817_C|T, 4850_C|T, 4889_C|T, 4952_C|T, 5000_T|C, 5060_T|C, 5198_T|C, 5362_T|C, 5369_C|T, 5375_A|G, 5387_C|T, 5501_A|G, 5546_T|C, 5591_T|C, 5744_A|G, 5828_T|C,
5937_T|C, 5987_G|C, 6056_C|T, 6101_T|C, 6152_C|T, 6155_A|G, 6164_C|T, 6275_A|C, 6359_C|T, 6363_C|T, 6473_T|A, 6684_A|C, 6785_T|C, 6807_T|C, 6890_A|G, 6979_A|G, 6983_A|G, 7037_C|T, 7050_T|C,
7064_T|C, 7079_A|G, 7085_A|C, 7358_T|C, 7367_A|G, 7451_A|C, 7517_C|T, 7633_T|C, 7637_A|G, 7739_C|T, 7805_T|C, 7898_C|T, 8007_G|A, 8105_C|T, 8126_T|C, 8408_T|C, 8516_A|G, 8606_C|T, 8651_C|T,
9017_T|C, 9098_T|C, 9206_A|G, 9222_G|A, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9473_G|A, 9500_T|C, 9503_C|T, 9509_T|C, 9527_A|G, 9582_C|T, 9591_T|C, 9620_C|T, 9623_C|T, 9806_C|T, 9926_T|C,
10161_G|A, 10376_G|A, 10392_A|G, 10409_A|G, 10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): MW122413.1




Target: 995 samples       Number of changes: 56                                                   


BC: A.1 + A.1             BC BR: 13-14                   BC BR coord: 3136 - 3137          


Direction L1: <<          Initial region span: 1-10,20-56Gap history (edge excluded): 10-20


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 1.85e-01                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 10 0.826549 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 20 5.883501 None None None * * *



Target sequence

, 254_A|G, 1380_C|T, 1616_C|T, 1904_C|T, 2093_T|C, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3014_T|C, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3459_C|T, 3534_G|A,
3617_G|A, 3731_C|T, 3863_G|A, 4536_A|G, 4556_A|T, 4697_T|C, 4706_A|G, 4784_G|A, 4914_C|G, 5195_G|A, 5315_A|G, 5597_C|T, 5894_G|A, 5937_T|C, 5966_C|T, 6029_G|A, 6299_C|T, 6327_A|C, 6725_T|C,
6737_C|T, 6755_C|T, 6779_T|C, 6904_T|C, 6983_A|G, 7451_A|C, 7505_C|T, 7633_T|C, 7689_C|T, 7805_T|C, 7922_G|A, 8690_A|G, 9240_C|T, 9305_C|T, 9353_T|C, 10052_T|C, 10169_A|C, 10361_T|C
 Case 3 (A.1): MT507047.1




Target: 995 samples       Number of changes: 44                                                 


BC: A.1 + A.1             BC BR: 8-9                    BC BR coord: 2404 - 2405         


Direction L1: <<          Initial region span: 1-5,11-44Gap history (edge excluded): 5-11


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 2.89e-03                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 5 0.687858 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 11 3.85001 None None None * * *



Target sequence

, 254_A|G, 637_T|C, 869_C|A, 968_G|A, 1115_T|C, 1616_C|T, 2192_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2978_T|C, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3617_G|A,
3731_C|T, 3863_G|A, 4607_A|G, 4731_G|A, 4784_G|A, 5087_T|C, 5195_G|A, 5315_A|G, 5937_T|C, 6327_A|C, 6725_T|C, 6737_C|T, 6983_A|G, 7223_A|G, 7307_T|C, 7451_A|C, 7633_T|C, 7667_T|C, 7805_T|C,
8480_A|G, 9240_C|T, 9246_C|T, 9305_C|T, 9353_T|C, 10561_T|C
 Case 3 (A.1): MT507048.1




Target: 995 samples       Number of changes: 44                                                 


BC: A.1 + A.1             BC BR: 5-6                    BC BR coord: 1990 - 1991         


Direction L1: <<          Initial region span: 1-4,10-44Gap history (edge excluded): 4-10


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 2.89e-03                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 4 0.452528 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 10 3.812157 None None None * * *



Target sequence

, 254_A|G, 637_T|C, 968_G|A, 1115_T|C, 1616_C|T, 2192_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 2978_T|C, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3617_G|A,
3731_C|T, 3863_G|A, 4607_A|G, 4731_G|A, 4784_G|A, 5087_T|C, 5195_G|A, 5315_A|G, 5937_T|C, 6327_A|C, 6725_T|C, 6737_C|T, 6983_A|G, 7223_A|G, 7307_T|C, 7451_A|C, 7633_T|C, 7667_T|C, 7805_T|C,
8480_A|G, 9240_C|T, 9246_C|T, 9305_C|T, 9353_T|C, 10561_T|C
 Case 3 (A.1): MT507049.1




Target: 995 samples       Number of changes: 46                                                 


BC: A.1 + A.1             BC BR: 6-7                    BC BR coord: 1174 - 1175         


Direction L1: <<          Initial region span: 1-6,12-46Gap history (edge excluded): 6-12


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 2.89e-03                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 0.923188 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 12 4.005297 None None None * * *



Target sequence

, 254_A|G, 256_T|C, 637_T|C, 869_C|A, 968_G|A, 1115_T|C, 1616_C|T, 2192_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2978_T|C, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A,
3617_G|A, 3731_C|T, 3863_G|A, 3895_C|T, 4607_A|G, 4731_G|A, 4784_G|A, 5087_T|C, 5195_G|A, 5315_A|G, 5937_T|C, 6327_A|C, 6725_T|C, 6737_C|T, 6983_A|G, 7223_A|G, 7307_T|C, 7451_A|C, 7633_T|C,
7667_T|C, 7805_T|C, 8480_A|G, 9240_C|T, 9246_C|T, 9305_C|T, 9353_T|C, 10561_T|C
 Case 3 (A.1): MT507050.1




Target: 995 samples       Number of changes: 46                                                 


BC: A.1 + A.1             BC BR: 6-7                    BC BR coord: 1174 - 1175         


Direction L1: <<          Initial region span: 1-6,12-46Gap history (edge excluded): 6-12


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 2.89e-03                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 0.923188 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 12 4.005297 None None None * * *



Target sequence

, 254_A|G, 256_T|C, 637_T|C, 869_C|A, 968_G|A, 1115_T|C, 1616_C|T, 2192_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2788_G|C, 2978_T|C, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A,
3617_G|A, 3731_C|T, 3863_G|A, 3895_C|T, 4607_A|G, 4731_G|A, 4784_G|A, 5087_T|C, 5195_G|A, 5315_A|G, 5937_T|C, 6327_A|C, 6725_T|C, 6737_C|T, 6983_A|G, 7223_A|G, 7307_T|C, 7451_A|C, 7633_T|C,
7667_T|C, 7805_T|C, 8480_A|G, 9240_C|T, 9246_C|T, 9305_C|T, 9353_T|C, 10561_T|C
 Case 3 (A.1): PP626400.1




Target: 995 samples          Number of changes: 173                                                                    


BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 16-17, 169-170                   BC BR coord: 1240 - 1241, 10391 - 10392    


Direction L1: <<             Initial region span: 1-7,123-169,170-173Gap history (edge excluded): 7-170 -> 7-123


Alt. candidates: [], []                                                                                                       


Model 1BP/2BP comparison:    2BP vs 1BP: 3.22e-253                                                                            


Rec. model vs L1: 0.00e+00   Rec. model vs L2: 1.13e+04                                                                


Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 7 1.128689 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 123 3.313539 NaN NaN NaN * * *
A.1.NmC1 181 169 -10.000000 -584.686256 1541.372512 3.218864e-253
A.1.NmC2 83 169 -10.000000 -1272.796736 2917.593472 0.000000e+00
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 170 1.925944 NaN NaN NaN * * *
A.1 995 123 1.574285 -6.660691 57.321382 0.367879 *



Target sequence

, 254_A|G, 423_G|A, 434_T|C, 437_C|T, 467_T|C, 523_A|G, 558_T|C, 575_T|C, 653_G|A, 719_T|C, 786_C|T, 803_A|G, 884_A|G, 962_T|C, 1133_C|T, 1175_A|G, 1263_T|C, 1325_C|T, 1436_T|C, 1466_T|C,
1616_C|T, 1688_C|T, 1718_C|T, 1739_T|G, 1896_T|C, 1922_C|T, 2060_T|A, 2066_C|T, 2132_T|C, 2207_A|G, 2375_C|T, 2394_A|T, 2411_C|T, 2448_T|C, 2460_T|C, 2471_A|G, 2492_T|C, 2519_G|A, 2525_G|A,
2576_G|A, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C, 2799_T|C, 2804_C|T, 2846_G|A, 2925_G|A, 2960_T|C, 2973_G|A, 3002_T|C, 3038_T|C, 3059_G|A, 3086_C|T, 3110_T|C, 3127_A|G, 3137_T|C,
3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3266_C|T, 3308_T|C, 3332_G|A, 3344_C|T, 3518_C|T, 3534_G|A, 3731_C|T, 3884_TT|CC, 3989_T|C, 4017_C|T, 4085_T|C, 4238_C|T, 4277_T|G, 4295_A|G,
4298_T|C, 4379_C|T, 4454_G|A, 4493_C|T, 4523_G|A, 4595_C|T, 4652_A|G, 4733_T|C, 4844_G|C, 4850_C|T, 4887_C|T, 4889_C|T, 4952_C|T, 5000_T|C, 5060_T|C, 5081_C|A, 5177_G|A, 5198_T|C, 5267_T|C,
5369_C|T, 5375_A|G, 5387_C|T, 5501_A|G, 5546_T|C, 5591_T|C, 5744_A|G, 5828_T|C, 5906_G|A, 5937_T|C, 5987_G|T, 6056_C|T, 6101_T|C, 6155_A|G, 6164_C|T, 6275_A|C, 6363_C|T, 6413_T|C, 6473_T|A,
6684_A|C, 6807_T|C, 6890_A|G, 6909_A|G, 6911_C|T, 6983_A|G, 7050_T|C, 7064_T|C, 7079_A|G, 7313_T|A, 7355_T|C, 7358_T|C, 7367_A|G, 7451_A|C, 7506_C|T, 7517_C|T, 7633_T|C, 7637_A|G, 7739_C|T,
7805_T|C, 7898_C|T, 8006_CG|TA, 8183_T|G, 8408_T|C, 8516_A|G, 8525_C|T, 8606_C|T, 8651_CC|TT, 8753_T|A, 8969_T|C, 9017_T|C, 9098_T|C, 9113_T|C, 9206_A|G, 9222_G|A, 9305_C|T, 9353_T|C,
9366_T|C, 9434_A|G, 9455_G|A, 9473_G|A, 9509_T|C, 9527_A|G, 9582_C|T, 9591_T|C, 9620_C|T, 9623_C|T, 9806_C|T, 9863_C|T, 9926_T|C, 10079_A|G, 10161_G|A, 10262_T|C, 10376_G|A, 10392_A|G,
10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): MW122450.1




Target: 995 samples       Number of changes: 54                                                   


BC: A.1 + A.1             BC BR: 49-50                   BC BR coord: 9751 - 9752          


Direction L1: >>          Initial region span: 1-46,50-54Gap history (edge excluded): 46-50


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 7.07e-06                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 46 5.322527 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 50 0.474372 None None None * * *



Target sequence

, 254_A|G, 1380_C|T, 1616_C|T, 1904_C|T, 2093_T|C, 2375_C|T, 2555_T|C, 2681_G|A, 2724_T|C, 2788_G|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3617_G|A, 3731_C|T,
3863_G|A, 4536_A|G, 4556_A|T, 4697_T|C, 4706_A|G, 4784_G|A, 5195_G|A, 5315_A|G, 5597_C|T, 5937_T|C, 5966_C|T, 6029_G|A, 6299_C|T, 6327_A|C, 6725_T|C, 6737_C|T, 6755_C|T, 6779_T|C, 6983_A|G,
7451_A|C, 7505_C|T, 7541_C|A, 7633_T|C, 7689_C|T, 7805_T|C, 8690_A|G, 9240_C|T, 9305_C|T, 9353_T|C, 9728_A|G, 9896_T|C, 10052_T|C, 10188_T|C, 10273_T|C, 10307_A|G
 Case 3 (A.1): OP858751.1




Target: 995 samples       Number of changes: 40                                                   


BC: A.1 + A.1             BC BR: 20-21                   BC BR coord: 3898 - 3899          


Direction L1: <<          Initial region span: 1-18,21-40Gap history (edge excluded): 18-21


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 1.30e-08                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 18 1.293618 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 21 2.809125 None None None * * *



Target sequence

, 254_A|G, 734_A|G, 1124_A|G, 1298_T|C, 1616_C|T, 1644_T|C, 2375_C|T, 2788_G|C, 2918_C|T, 2925_G|A, 3059_G|A, 3131_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3534_G|A, 3617_G|A, 3731_C|T,
3752_C|T, 4469_T|C, 4784_G|A, 5195_G|A, 5315_A|G, 5937_T|C, 6327_A|C, 6429_C|T, 6725_T|C, 6737_C|T, 6983_A|G, 7633_T|C, 7805_T|C, 7925_C|T, 8177_T|C, 8663_C|A, 9240_C|T, 9305_C|T, 9353_T|C,
9362_G|A, 10561_T|C
 Case 3 (A.1): MT377493.2




Target: 995 samples          Number of changes: 173                                                                    


BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 16-17, 169-170                   BC BR coord: 1240 - 1241, 10391 - 10392    


Direction L1: <<             Initial region span: 1-7,123-169,170-173Gap history (edge excluded): 7-170 -> 7-123


Alt. candidates: [], []                                                                                                       


Model 1BP/2BP comparison:    2BP vs 1BP: 3.22e-253                                                                            


Rec. model vs L1: 0.00e+00   Rec. model vs L2: 1.13e+04                                                                


Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 7 1.128689 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 123 3.313539 NaN NaN NaN * * *
A.1.NmC1 181 169 -10.000000 -584.686256 1541.372512 3.218864e-253
A.1.NmC2 83 169 -10.000000 -1272.796736 2917.593472 0.000000e+00
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 170 1.925944 NaN NaN NaN * * *
A.1 995 123 1.574285 -6.660691 57.321382 0.367879 *



Target sequence

, 254_A|G, 423_G|A, 434_T|C, 437_C|T, 467_T|C, 523_A|G, 558_T|C, 575_T|C, 653_G|A, 719_T|C, 786_C|T, 803_A|G, 884_A|G, 962_T|C, 1133_C|T, 1175_A|G, 1263_T|C, 1325_C|T, 1436_T|C, 1466_T|C,
1616_C|T, 1688_C|T, 1718_C|T, 1739_T|G, 1896_T|C, 1922_C|T, 2060_T|A, 2066_C|T, 2132_T|C, 2207_A|G, 2375_C|T, 2394_A|T, 2411_C|T, 2448_T|C, 2460_T|C, 2471_A|G, 2492_T|C, 2519_G|A, 2525_G|A,
2576_G|A, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C, 2799_T|C, 2804_C|T, 2846_G|A, 2925_G|A, 2960_T|C, 2973_G|A, 3002_T|C, 3038_T|C, 3059_G|A, 3086_C|T, 3110_T|C, 3127_A|G, 3137_T|C,
3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3266_C|T, 3308_T|C, 3332_G|A, 3344_C|T, 3518_C|T, 3534_G|A, 3731_C|T, 3884_TT|CC, 3989_T|C, 4017_C|T, 4085_T|C, 4238_C|T, 4277_T|G, 4295_A|G,
4298_T|C, 4379_C|T, 4454_G|A, 4493_C|T, 4523_G|A, 4595_C|T, 4652_A|G, 4733_T|C, 4844_G|C, 4850_C|T, 4887_C|T, 4889_C|T, 4952_C|T, 5000_T|C, 5060_T|C, 5081_C|A, 5177_G|A, 5198_T|C, 5267_T|C,
5369_C|T, 5375_A|G, 5387_C|T, 5501_A|G, 5546_T|C, 5591_T|C, 5744_A|G, 5828_T|C, 5906_G|A, 5937_T|C, 5987_G|T, 6056_C|T, 6101_T|C, 6155_A|G, 6164_C|T, 6275_A|C, 6363_C|T, 6413_T|C, 6473_T|A,
6684_A|C, 6807_T|C, 6890_A|G, 6909_A|G, 6911_C|T, 6983_A|G, 7050_T|C, 7064_T|C, 7079_A|G, 7313_T|A, 7355_T|C, 7358_T|C, 7367_A|G, 7451_A|C, 7506_C|T, 7517_C|T, 7633_T|C, 7637_A|G, 7739_C|T,
7805_T|C, 7898_C|T, 8006_CG|TA, 8183_T|G, 8408_T|C, 8516_A|G, 8525_C|T, 8606_C|T, 8651_CC|TT, 8753_T|A, 8969_T|C, 9017_T|C, 9098_T|C, 9113_T|C, 9206_A|G, 9222_G|A, 9305_C|T, 9353_T|C,
9366_T|C, 9434_A|G, 9455_G|A, 9473_G|A, 9509_T|C, 9527_A|G, 9582_C|T, 9591_T|C, 9620_C|T, 9623_C|T, 9806_C|T, 9863_C|T, 9926_T|C, 10079_A|G, 10161_G|A, 10262_T|C, 10376_G|A, 10392_A|G,
10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): MK829152.1




Target: 995 samples       Number of changes: 30                                                 


BC: A.1 + A.1             BC BR: 7-8                    BC BR coord: 2723 - 2724         


Direction L1: <<          Initial region span: 1-4,14-30Gap history (edge excluded): 4-14


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 4.09e-09                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 4 0.686929 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 14 1.615582 None None None * * *



Target sequence

, 254_A|G, 510_T|C, 647_G|A, 1418_G|A, 1616_C|T, 2117_A|G, 2225_A|G, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3254_T|C, 3332_G|A, 3428_C|T, 3731_C|T, 5937_T|C, 6896_T|C, 6930_T|C, 7242_A|G,
7451_A|C, 7478_C|T, 7596_A|C, 7633_T|C, 7805_T|C, 7877_C|T, 7922_G|A, 8024_T|C, 9305_C|T, 9334_A|G, 9353_T|C
 Case 3 (A.1): MT078742.1




Target: 995 samples       Number of changes: 36                                                 


BC: A.1 + A.1             BC BR: 4-5                    BC BR coord: 1397 - 1398         


Direction L1: <<          Initial region span: 1-4,19-36Gap history (edge excluded): 4-19


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 2.69e-07                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 4 0.939106 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 19 2.379888 None None None * * *



Target sequence

, 419_A|G, 467_T|C, 1044_G|A, 1313_C|T, 1616_C|T, 2375_C|T, 2681_G|A, 2724_T|C, 2853_T|C, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3459_C|T, 3534_G|A, 3731_C|T, 3987_G|A,
4193_A|G, 4367_T|C, 5676_C|T, 5937_T|C, 6958_A|G, 6983_A|G, 6992_A|G, 7229_A|G, 7442_A|G, 7451_A|C, 7633_T|C, 7805_T|C, 8762_A|G, 8777_C|T, 9305_C|T, 9353_T|C, 9557_T|C
 Case 3 (A.1): MH063259.1




Target: 995 samples       Number of changes: 36                                                 


BC: A.1 + A.1             BC BR: 7-8                    BC BR coord: 2798 - 2799         


Direction L1: <<          Initial region span: 1-7,15-36Gap history (edge excluded): 7-15


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison: 1BP vs 2BP: 4.99e-07                                                         


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                            


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 7 0.588154 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 15 2.721124 None None None * * *



Target sequence

, 254_A|G, 734_A|G, 1616_C|T, 2375_C|T, 2669_T|C, 2681_G|A, 2788_G|C, 2925_G|A, 3059_G|A, 3070_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3470_T|C, 3505_A|G, 3534_G|A, 3731_C|T, 3863_G|A,
4161_G|A, 5195_G|A, 5315_A|G, 5840_T|C, 6429_C|T, 6725_T|C, 6737_C|T, 6983_A|G, 7451_A|C, 7633_T|C, 7925_C|T, 9240_C|T, 9344_G|A, 9353_T|C, 9635_G|T, 10127_T|G, 10301_T|G
 Case 3 (A.1): MH063263.1




Target: 995 samples       Number of changes: 47                                                   


BC: A.1 + A.1             BC BR: 39-40                   BC BR coord: 7516 - 7517          


Direction L1: >>          Initial region span: 1-36,42-47Gap history (edge excluded): 36-42


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 3.33e-07                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 36 2.817295 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 42 0.257366 None None None * * *



Target sequence

, 254_A|G, 734_A|G, 825_T|C, 1616_C|T, 2375_C|T, 2669_T|C, 2681_G|A, 2724_T|C, 2729_A|G, 2788_G|C, 2918_C|T, 2925_G|A, 3059_G|A, 3070_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A, 3470_T|C,
3534_G|A, 3617_G|A, 3731_C|T, 3863_G|A, 4161_G|A, 4470_G|T, 4523_G|T, 4784_G|A, 4790_A|G, 5195_G|A, 5315_A|G, 5424_C|T, 5937_T|C, 6327_A|C, 6429_C|T, 6725_T|C, 6737_C|T, 6983_A|G, 7050_T|C,
7451_A|C, 7633_T|C, 7805_T|C, 7853_G|A, 7925_C|T, 8237_T|C, 9344_G|A, 9353_T|C, 9778_A|G
 Case 3 (A.1): MK829154.1




Target: 995 samples       Number of changes: 42                                                   


BC: A.1 + A.1             BC BR: 26-27                   BC BR coord: 5936 - 5937          


Direction L1: >>          Initial region span: 1-20,34-42Gap history (edge excluded): 20-34


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 1.36e-02                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 20 1.680559 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 34 1.542976 None None None * * *



Target sequence

, 254_A|G, 485_T|C, 569_T|C, 791_A|G, 1616_C|T, 1883_C|T, 2060_T|C, 2225_A|G, 2285_C|A, 2375_C|T, 2681_G|A, 2724_T|C, 2840_T|A, 2925_G|A, 3059_G|A, 3140_A|G, 3186_G|A, 3218_T|A, 3332_G|A,
3428_C|T, 3722_T|C, 3731_C|T, 4128_T|C, 4730_A|G, 4919_C|T, 5330_T|C, 6930_T|C, 7242_A|G, 7451_A|C, 7478_C|T, 7633_T|C, 7805_T|C, 8249_C|T, 8648_G|A, 8867_C|T, 8897_A|G, 9219_T|C, 9305_C|T,
9334_A|G, 9353_T|C, 9929_T|C, 10139_C|G
 Case 3 (A.1): OQ661918.1




Target: 995 samples       Number of changes: 173                                                     


BC: A.1 + A.1.NmC1        BC BR: 167-168                   BC BR coord: 10288 - 10289         


Direction L1: >>          Initial region span: 1-55,171-173Gap history (edge excluded): 55-171


Alt. candidates: [], []                                                                                     


Model 1BP/2BP comparison: 1BP vs 2BP: 3.14e-02                                                              


Rec. model vs L1: 1.88e+14Rec. model vs L2: 0.00e+00                                                 


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 55 2.650942 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 171 1.972602 NaN NaN NaN * * *
A.1 995 155 1.306556 -1.268593 16.537187 1.328857e+08 *



Target sequence

, 212_C|T, 254_A|G, 423_G|A, 467_T|C, 523_A|G, 558_T|C, 575_T|C, 653_G|A, 719_T|C, 800_G|A, 803_A|G, 884_A|G, 1031_G|T, 1175_A|G, 1325_C|T, 1370_G|A, 1388_C|T, 1598_T|C, 1611_T|C, 1616_C|T,
1718_C|T, 1784_T|C, 1814_T|C, 1875_T|C, 1896_T|C, 1922_C|T, 2060_T|A, 2066_C|T, 2132_T|C, 2207_A|G, 2233_A|G, 2279_T|C, 2375_C|T, 2394_A|T, 2411_C|T, 2435_T|C, 2460_T|C, 2492_T|C, 2519_G|A,
2525_G|A, 2576_G|A, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C, 2804_C|T, 2846_G|A, 2925_G|A, 2960_T|C, 2973_G|A, 3002_T|C, 3038_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A,
3203_G|A, 3218_T|A, 3254_T|C, 3266_C|T, 3290_A|T, 3308_T|C, 3332_G|A, 3344_C|T, 3491_G|A, 3500_C|T, 3518_C|T, 3534_G|A, 3731_C|T, 3885_T|C, 3917_C|A, 3945_T|C, 3989_T|C, 4085_T|C, 4238_C|T,
4295_A|G, 4415_T|C, 4454_G|A, 4493_C|T, 4523_G|A, 4595_C|T, 4607_A|G, 4652_A|G, 4733_T|C, 4781_C|T, 4817_C|T, 4889_C|T, 4952_C|T, 5000_T|C, 5060_T|C, 5195_G|A, 5198_T|C, 5362_T|C, 5369_C|T,
5375_A|G, 5387_C|T, 5501_A|G, 5546_T|C, 5591_T|C, 5744_A|G, 5810_A|G, 5828_T|C, 5937_T|C, 5987_G|C, 6056_C|T, 6083_A|T, 6101_T|C, 6152_C|T, 6155_A|G, 6164_C|T, 6275_A|C, 6359_C|T, 6363_C|T,
6473_T|A, 6684_A|C, 6785_T|C, 6807_T|C, 6890_A|G, 6983_A|G, 7037_C|T, 7050_T|C, 7064_T|C, 7079_A|G, 7085_A|C, 7358_T|C, 7367_A|G, 7451_A|C, 7517_C|T, 7633_T|C, 7637_A|G, 7739_C|T, 7805_T|C,
7898_C|T, 8007_G|A, 8105_C|T, 8126_T|C, 8402_C|T, 8408_T|C, 8516_A|G, 8555_C|T, 8606_C|T, 8618_A|G, 8651_C|T, 8933_T|C, 9017_T|C, 9098_T|C, 9206_A|G, 9222_G|A, 9305_C|T, 9353_T|C, 9434_A|G,
9455_G|A, 9473_G|A, 9503_C|T, 9509_T|C, 9527_A|G, 9545_G|A, 9582_C|T, 9591_T|C, 9620_C|T, 9623_C|T, 9682_T|C, 9806_C|T, 9926_T|C, 10161_G|A, 10376_G|A, 10392_A|G, 10409_A|G, 10477_T|C,
10561_T|C, 10613_C|T
 Case 3 (A.1): MK238035.1




Target: 995 samples        Number of changes: 151                                                   


BC: A.1 + A.1.NmC1         BC BR: 145-146                  BC BR coord: 10288 - 10289        


Direction L1: <<           Initial region span: 1-6,149-151Gap history (edge excluded): 6-149


Alt. candidates: [], []                                                                                    


Model 1BP/2BP comparison:  -                                                                               


Rec. model vs L1: 8.07e+20 Rec. model vs L2: 0.00e+00                                               


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 1.085531 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 149 3.420355 NaN NaN NaN * * *
A.1 995 113 0.536540 -1.235803 16.471607 6.797562e+11 *



Target sequence

, 188_T|C, 254_A|G, 290_A|G, 299_T|C, 423_G|A, 432_A|G, 523_A|G, 558_T|C, 653_G|A, 719_T|C, 773_T|C, 803_A|G, 884_A|G, 947_C|T, 953_AC|GT, 968_G|A, 1175_A|G, 1559_A|G, 1568_C|T, 1616_C|T,
1787_T|C, 1815_G|A, 1854_C|T, 2066_C|T, 2375_C|T, 2411_C|T, 2448_T|C, 2504_G|A, 2525_G|A, 2606_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2739_G|A, 2774_C|T, 2795_G|A, 2879_T|C, 2925_G|A, 2949_C|A,
2969_C|T, 2984_T|C, 3038_T|C, 3041_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3228_T|C, 3248_T|C, 3254_T|C, 3332_G|A, 3335_C|T, 3518_C|T, 3534_G|A, 3566_T|C, 3596_G|A,
3671_A|G, 3722_T|C, 3731_C|T, 3836_T|C, 3857_C|T, 3881_T|C, 3989_T|C, 4070_T|C, 4085_T|C, 4106_A|G, 4220_G|A, 4322_C|T, 4337_A|G, 4403_A|C, 4409_A|G, 4454_G|A, 4499_C|T, 4523_G|A, 4652_A|G,
4916_C|T, 4925_G|A, 4934_G|A, 5000_T|C, 5030_C|T, 5060_T|C, 5096_T|C, 5279_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5421_C|T, 5459_T|C, 5555_C|T, 5591_T|C, 5642_A|G, 5717_C|T, 5798_C|T, 5828_T|C,
5937_T|C, 6020_T|C, 6056_C|T, 6122_C|T, 6143_T|C, 6545_C|T, 6684_A|C, 6807_T|C, 6827_T|A, 6839_G|A, 6983_A|G, 7050_T|C, 7223_A|G, 7316_T|C, 7451_A|C, 7517_C|T, 7568_T|C, 7592_T|C, 7598_G|A,
7633_T|C, 7637_A|G, 7646_C|T, 7880_G|A, 7887_T|C, 7895_G|A, 7964_A|G, 8007_G|A, 8018_A|G, 8063_C|T, 8069_T|C, 8303_C|T, 8467_T|C, 8474_C|T, 8591_A|G, 8606_C|T, 8631_A|G, 8780_T|C, 9011_C|T,
9017_T|C, 9080_C|A, 9239_T|C, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9515_C|T, 9539_T|C, 9614_G|A, 10146_G|A, 10322_C|T, 10335_G|A, 10376_G|A, 10392_A|G, 10477_T|C, 10561_T|C
 Case 3 (A.1): MK238037.1




Target: 995 samples       Number of changes: 152                                                                


BC: A.1 + A.1.NmC1 + A.1  BC BR: 5-6, 9-10                    BC BR coord: 427 - 428, 754 - 755          


Direction L1: <<          Initial region span: 1-5,6-8,113-152Gap history (edge excluded): 5-113 -> 8-113


Alt. candidates: [], []                                                                                                


Model 1BP/2BP comparison: 2BP vs 1BP: 1.39e-02                                                                         


Rec. model vs L1: 1.38e-02Rec. model vs L2: 0.00e+00                                                            


Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 5 0.8502 None None None * * *
|||||

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 8 4.667316 NaN NaN NaN * * *
A.1 995 6 0.000000 -2.560621 15.121243 5.117957e-03 *
A.1.NmC2 83 6 -2.355267 -42.355267 94.710534 2.668995e-20
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 113 1.287263 None None None * * *



Target sequence

, 188_T|C, 254_A|G, 290_A|G, 299_T|C, 423_G|A, 523_A|G, 558_T|C, 653_G|A, 719_T|C, 773_T|C, 803_A|G, 884_A|G, 947_C|T, 953_AC|GT, 968_G|A, 1175_A|G, 1559_A|G, 1568_C|T, 1616_C|T, 1787_T|C,
1815_G|A, 2066_C|T, 2375_C|T, 2411_C|T, 2448_T|C, 2504_G|A, 2525_G|A, 2606_C|T, 2654_C|T, 2681_G|A, 2700_G|A, 2724_T|C, 2739_G|A, 2774_C|T, 2795_G|A, 2879_T|C, 2925_G|A, 2949_C|A, 2969_C|T,
2984_T|C, 3038_T|C, 3041_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3228_T|C, 3254_T|C, 3332_G|A, 3518_C|T, 3534_G|A, 3566_T|C, 3596_G|A, 3671_A|G, 3731_C|T, 3836_T|C,
3857_C|T, 3881_T|C, 3989_T|C, 4070_T|C, 4085_T|C, 4106_A|G, 4133_A|T, 4220_G|A, 4322_C|T, 4337_A|G, 4403_A|C, 4409_A|G, 4454_G|A, 4499_C|T, 4523_G|A, 4925_G|A, 4934_G|A, 5000_T|C, 5030_C|T,
5060_T|C, 5096_T|C, 5277_T|C, 5279_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5421_C|T, 5459_T|C, 5519_A|C, 5555_C|T, 5591_T|C, 5642_A|G, 5717_C|T, 5798_C|T, 5828_T|C, 5937_T|C, 6020_T|C, 6056_C|T,
6143_T|C, 6545_C|T, 6626_C|T, 6642_T|C, 6684_A|C, 6807_T|C, 6827_T|A, 6839_G|A, 6908_T|A, 6983_A|G, 7046_T|G, 7050_T|C, 7316_T|C, 7451_A|C, 7502_G|A, 7517_C|T, 7568_T|C, 7598_G|A, 7633_T|C,
7637_A|G, 7646_C|T, 7808_T|C, 7880_G|A, 7887_T|C, 7895_G|A, 7964_A|G, 8007_G|A, 8018_A|G, 8063_C|T, 8069_T|C, 8303_C|T, 8408_T|C, 8467_T|C, 8474_C|T, 8510_C|T, 8591_A|G, 8606_C|T, 8631_A|G,
8780_T|C, 9011_C|T, 9017_T|C, 9239_T|C, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9515_C|T, 9539_T|C, 9591_T|C, 9614_G|A, 10193_A|G, 10322_C|T, 10335_G|A, 10376_G|A, 10392_A|G, 10561_T|C
 Case 3 (A.1): MK238039.1




Target: 995 samples       Number of changes: 91                                                   


BC: A.1 + A.1             BC BR: 71-72                   BC BR coord: 7450 - 7451          


Direction L1: >>          Initial region span: 1-27,87-91Gap history (edge excluded): 27-87


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison: 1BP vs 2BP: 7.24e-23                                                           


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                              


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 27 0.820835 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 87 0.231162 None None None * * *



Target sequence

, 719_T|C, 773_T|C, 803_A|G, 884_A|G, 947_C|T, 953_AC|GT, 968_G|A, 1175_A|G, 1559_A|G, 1568_C|T, 1616_C|T, 2066_C|T, 2375_C|T, 2411_C|T, 2448_T|C, 2504_G|A, 2525_G|A, 2606_C|T, 2654_C|T,
2681_G|A, 2700_G|A, 2724_T|C, 2739_G|A, 2742_C|A, 2774_C|T, 2795_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3228_T|C, 3254_T|C, 3332_G|A, 3518_C|T, 3534_G|A, 3671_A|G, 3731_C|T,
3836_T|C, 3857_C|T, 3881_T|C, 3989_T|C, 4403_A|C, 4409_A|G, 4454_G|A, 4499_C|T, 4523_G|A, 4934_G|A, 5000_T|C, 5030_C|T, 5060_T|C, 5277_T|C, 5279_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5421_C|T,
5459_T|C, 5642_A|G, 5717_C|T, 5798_C|T, 5828_T|C, 5937_T|C, 6020_T|C, 6056_C|T, 6143_T|C, 6807_T|C, 6827_T|A, 6839_G|A, 7046_T|G, 7050_T|C, 7502_G|A, 7517_C|T, 7568_T|C, 7598_G|A, 7633_T|C,
7637_A|G, 7646_C|T, 8780_T|C, 9239_T|C, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9591_T|C, 9614_G|A, 10245_A|T, 10322_C|T, 10335_G|A, 10376_G|A, 10392_A|G
 Case 3 (A.1): MK238038.1




Target: 995 samples       Number of changes: 146                                                                


BC: A.1 + A.1.NmC1 + A.1  BC BR: 5-6, 9-10                    BC BR coord: 427 - 428, 754 - 755          


Direction L1: <<          Initial region span: 1-5,6-8,111-146Gap history (edge excluded): 5-111 -> 8-111


Alt. candidates: [], []                                                                                                


Model 1BP/2BP comparison: 2BP vs 1BP: 2.79e-01                                                                         


Rec. model vs L1: 1.39e-02Rec. model vs L2: 0.00e+00                                                            


Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 5 1.123655 None None None * * *
|||||

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 8 4.667316 NaN NaN NaN * * *
A.1 995 6 0.000000 -2.560621 15.121243 5.117957e-03 *
A.1.NmC2 83 6 -2.355267 -42.355267 94.710534 2.668995e-20
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 111 2.09327 None None None * * *



Target sequence

, 188_T|C, 290_A|G, 299_T|C, 333_G|A, 423_G|A, 523_A|G, 558_T|C, 653_G|A, 719_T|C, 773_T|C, 803_A|G, 884_A|G, 947_C|T, 953_AC|GT, 968_G|A, 1175_A|G, 1559_A|G, 1568_C|T, 1616_C|T, 1787_T|C,
1815_G|A, 2066_C|T, 2375_C|T, 2411_C|T, 2448_T|C, 2504_G|A, 2525_G|A, 2606_C|T, 2654_C|T, 2681_G|A, 2700_G|A, 2724_T|C, 2739_G|A, 2774_C|T, 2795_G|A, 2879_T|C, 2925_G|A, 2949_C|A, 2969_C|T,
2984_T|C, 3038_T|C, 3041_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3228_T|C, 3254_T|C, 3332_G|A, 3518_C|T, 3534_G|A, 3566_T|C, 3596_G|A, 3671_A|G, 3731_C|T, 3836_T|C,
3857_C|T, 3881_T|C, 3989_T|C, 4070_T|C, 4085_T|C, 4106_A|G, 4133_A|T, 4220_G|A, 4322_C|T, 4337_A|G, 4403_A|C, 4409_A|G, 4454_G|A, 4499_C|T, 4523_G|A, 4925_G|A, 4934_G|A, 5000_T|C, 5030_C|T,
5060_T|C, 5096_T|C, 5277_T|C, 5279_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5421_C|T, 5459_T|C, 5486_T|C, 5555_C|T, 5591_T|C, 5642_A|G, 5717_C|T, 5798_C|T, 5828_T|C, 5937_T|C, 5967_A|G, 6020_T|C,
6056_C|T, 6143_T|C, 6545_C|T, 6642_T|C, 6684_A|C, 6807_T|C, 6827_T|A, 6839_G|A, 6908_T|A, 6983_A|G, 7046_T|G, 7050_T|C, 7451_A|C, 7517_C|T, 7568_T|C, 7598_G|A, 7633_T|C, 7637_A|G, 7646_C|T,
7880_G|A, 7887_T|C, 7895_G|A, 7964_A|G, 8007_G|A, 8018_A|G, 8063_C|T, 8069_T|C, 8303_C|T, 8467_T|C, 8474_C|T, 8510_C|T, 8591_A|G, 8606_C|T, 8631_A|G, 8780_T|C, 9011_C|T, 9017_T|C, 9239_T|C,
9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9515_C|T, 9539_T|C, 10193_A|G, 10322_C|T, 10335_G|A, 10376_G|A, 10392_A|G, 10561_T|C
 Case 3 (A.1): MN611472.1




Target: 995 samples        Number of changes: 107                                                   


BC: A.1.NmC1 + A.1         BC BR: 6-7                      BC BR coord: 754 - 755            


Direction L1: <<           Initial region span: 1-6,104-107Gap history (edge excluded): 6-104


Alt. candidates: [], []                                                                                    


Model 1BP/2BP comparison:  -                                                                               


Rec. model vs L1: 0.00e+00 Rec. model vs L2: 2.37e+06                                               


Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 6 -8.607189 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 104 0.908531 None None None * * *



Target sequence

, 188_T|C, 254_A|G, 523_A|G, 558_T|C, 578_T|C, 653_G|A, 878_C|T, 1067_T|C, 1073_C|T, 1175_A|G, 1196_C|T, 1616_C|T, 1728_A|C, 1799_G|A, 2210_T|C, 2375_C|T, 2471_A|G, 2540_A|G, 2552_C|T,
2615_G|A, 2654_C|T, 2681_G|A, 2724_T|C, 2750_G|A, 2925_G|A, 3059_G|A, 3137_TC|CT, 3140_A|G, 3158_T|C, 3167_A|T, 3186_G|A, 3218_T|A, 3254_T|C, 3332_G|A, 3464_T|A, 3518_C|T, 3534_G|A, 3731_C|T,
3932_C|T, 4005_A|G, 4013_T|C, 4085_T|C, 4104_G|A, 4108_A|G, 4166_G|A, 4454_G|A, 4547_C|T, 4766_C|T, 4905_T|C, 5000_T|C, 5021_A|G, 5060_T|C, 5156_T|C, 5249_C|T, 5327_G|A, 5357_C|T, 5375_A|G,
5390_CT|TC, 5420_T|C, 5585_C|T, 5591_T|C, 5828_T|C, 5937_T|C, 6056_C|T, 6140_A|G, 6254_T|C, 6363_C|T, 6674_C|T, 6983_A|G, 6992_A|G, 7014_C|T, 7322_G|A, 7451_A|C, 7517_C|T, 7530_T|C, 7633_T|C,
7646_C|T, 7730_C|T, 7805_T|C, 7961_A|G, 8007_G|A, 8082_C|T, 8144_A|T, 8186_A|G, 8199_G|T, 8222_C|T, 8303_C|T, 8353_C|T, 8369_C|T, 8408_T|C, 8702_C|T, 8914_A|G, 8969_T|C, 9017_T|C, 9041_A|G,
9305_C|T, 9353_T|C, 9434_A|G, 9722_T|C, 9854_C|T, 10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T, 10647_T|C, 10649_T|C, 10652_AG|GA
 Case 3 (A.1): EU545988.1




Target: 995 samples       Number of changes: 205                                                   


BC: A.1 + A.1             BC BR: 136-137                  BC BR coord: 6580 - 6581          


Direction L1: <<          Initial region span: 1-8,141-205Gap history (edge excluded): 8-141


Alt. candidates: [], []                                                                                   


Model 1BP/2BP comparison: 1BP vs 2BP: 8.86e-16                                                            


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                               


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 8 1.46353 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 141 5.424392 None None None * * *



Target sequence

, 117_.|C, 122_A|G, 138, 254_A|G, 257_T|A, 423_G|A, 467_T|C, 475_C|T, 523_A|G, 558_T|C, 569_T|C, 578_T|C, 639_C|T, 653_G|A, 689_G|A, 719_T|C, 803_A|G, 827_C|T, 837_T|C, 902_T|C, 917_C|T,
1070_C|T, 1095_A|G, 1154_C|T, 1175_A|G, 1232_A|G, 1505_C|T, 1616_C|T, 1655_C|T, 1682_C|T, 1701_C|T, 1991_T|C, 2049_T|C, 2066_C|T, 2171_C|T, 2267_C|T, 2285_C|T, 2375_C|T, 2394_A|G, 2411_C|T,
2437_T|C, 2468_C|T, 2525_G|A, 2540_A|G, 2567_A|T, 2606_C|T, 2615_G|A, 2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3052_T|C, 3059_G|A, 3071_A|G, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A,
3218_T|A, 3254_T|C, 3275_C|T, 3332_G|A, 3434_G|A, 3518_C|T, 3534_G|A, 3710_T|C, 3731_C|T, 3740_C|T, 3806_A|T, 3854_A|G, 3870_T|C, 3875_C|T, 3885_T|C, 3989_T|C, 4011_G|A, 4016_T|G, 4040_A|G,
4085_T|C, 4091_C|T, 4106_A|G, 4109_A|G, 4128_T|C, 4146_C|T, 4154_A|C, 4238_C|T, 4259_C|T, 4271_A|G, 4277_T|C, 4295_A|G, 4454_G|A, 4457_A|G, 4481_G|A, 4493_C|T, 4523_G|A, 4592_A|G, 4595_C|T,
4706_A|T, 4733_T|C, 4751_T|C, 4850_C|T, 4859_A|G, 4871_T|C, 4948_T|C, 4988_G|A, 4995_C|T, 5000_T|C, 5060_T|C, 5066_C|T, 5081_C|A, 5163_C|T, 5193_T|C, 5369_C|T, 5375_A|G, 5384_C|T, 5387_C|T,
5429_G|A, 5468_T|C, 5546_T|C, 5567_G|C, 5591_T|C, 5800_A|T, 5811_C|A, 5828_T|C, 5937_T|C, 6056_C|T, 6092_C|T, 6101_T|C, 6164_C|T, 6292_G|A, 6363_C|T, 6389_G|A, 6443_G|A, 6473_T|C, 6501_C|T,
6506_A|G, 6588_A|G, 6618_C|T, 6629_T|C, 6684_A|C, 6689_C|T, 6698_A|C, 6746_C|T, 6882_G|A, 6890_A|G, 6902_C|T, 6923_C|T, 6935_G|A, 6983_A|G, 7037_C|T, 7049_CT|TC, 7064_T|C, 7085_A|G, 7157_C|T,
7208_A|G, 7405_C|A, 7408_A|G, 7451_A|C, 7517_C|T, 7568_T|C, 7633_T|C, 7679_A|G, 7713_T|C, 7733_G|A, 7805_T|C, 7817_G|A, 7853_G|T, 7869_C|A, 7871_G|A, 8007_G|A, 8093_G|T, 8105_C|T, 8162_C|T,
8408_T|C, 8450_T|C, 8516_A|G, 8606_C|T, 8813_G|A, 9011_C|T, 9017_T|C, 9119_T|C, 9122_A|G, 9176_C|T, 9266_A|T, 9275_T|A, 9305_C|T, 9353_T|C, 9413_T|C, 9434_A|G, 9455_G|A, 9503_C|T, 9509_T|C,
9518_A|G, 9527_A|G, 9677_G|A, 9734_T|C, 9779_C|T, 9884_G|A, 9896_T|A, 10244_C|T, 10262_T|C, 10281_G|A, 10361_T|C, 10367_T|C, 10374_C|T
 Case 3 (A.1): KU955593.1




Target: 995 samples        Number of changes: 176                                               


BC: A.1 + A.1.NmC1         BC BR: 172-173                    BC BR coord: 10391 - 10392  


Direction L1: >>           Initial region span: 1-172,173-176Gap history (edge excluded):


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison:  -                                                                           


Rec. model vs L1: 6.96e-02 Rec. model vs L2: 0.00e+00                                           


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 172 3.70039 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 173 3.420355 None None None * * *



Target sequence

, 122_A|G, 254_A|G, 359_C|T, 423_G|A, 467_T|C, 475_C|T, 496_G|A, 523_A|G, 558_T|A, 653_G|A, 719_T|C, 803_A|G, 837_T|C, 1070_C|T, 1175_A|G, 1337_A|T, 1343_C|T, 1442_C|T, 1616_C|T, 1655_C|T,
1736_A|G, 1922_C|T, 2066_C|T, 2093_T|C, 2111_T|G, 2156_G|A, 2282_A|G, 2285_C|T, 2298_T|C, 2375_C|T, 2394_A|G, 2411_C|T, 2525_G|A, 2570_C|T, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C,
2828_C|T, 2864_A|G, 2925_G|A, 3038_T|C, 3050_T|C, 3052_T|C, 3059_G|A, 3071_A|G, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3296_C|T, 3332_G|A, 3473_C|T, 3518_C|T,
3534_G|A, 3605_G|A, 3617_G|A, 3731_C|T, 3767_A|T, 3806_A|T, 3827_C|T, 3854_A|G, 3885_T|C, 3928_T|C, 3989_T|C, 4085_T|C, 4094_C|T, 4106_A|G, 4238_C|T, 4295_A|G, 4454_G|A, 4481_G|A, 4493_C|T,
4523_G|A, 4536_A|G, 4592_A|G, 4595_C|T, 4733_T|C, 4751_T|C, 4988_G|A, 5000_T|C, 5036_C|T, 5060_T|C, 5066_C|T, 5096_T|C, 5267_T|C, 5369_C|T, 5375_A|G, 5387_C|T, 5561_C|T, 5591_T|C, 5717_C|T,
5828_T|C, 5937_T|C, 6002_T|C, 6056_C|T, 6092_C|T, 6101_T|C, 6164_C|T, 6363_C|T, 6443_G|A, 6473_T|C, 6512_C|T, 6533_A|G, 6584_T|C, 6608_G|A, 6626_C|T, 6629_T|C, 6684_A|C, 6746_C|T, 6890_A|G,
6983_A|G, 6989_C|T, 7037_C|T, 7049_CT|TC, 7148_T|C, 7157_C|T, 7175_C|T, 7451_A|T, 7493_G|T, 7517_C|T, 7538_A|G, 7568_T|C, 7577_T|C, 7604_T|C, 7633_T|C, 7679_A|G, 7713_T|C, 7805_T|C, 7826_T|C,
7869_C|A, 7937_C|T, 8007_G|A, 8105_C|T, 8387_C|T, 8408_T|C, 8429_G|A, 8516_A|G, 8597_T|C, 8823_C|T, 8888_T|C, 9017_T|C, 9098_T|C, 9176_C|T, 9200_G|A, 9225_C|T, 9272_C|T, 9305_C|T, 9353_T|C,
9434_A|G, 9455_G|A, 9503_C|T, 9527_A|G, 9623_C|T, 9677_G|A, 9704_C|T, 9758_A|G, 9884_G|A, 9887_C|T, 9896_T|A, 9899_A|G, 10217_A|G, 10281_G|A, 10286_C|T, 10314_A|G, 10349_T|C, 10361_T|C,
10376_G|A, 10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): KX377336.1




Target: 995 samples       Number of changes: 469                                                                    


BC: A.1 + A.1.NmC1 + A.1  BC BR: 463-464, 466-467                   BC BR coord: 10391 - 10392, 10611 - 10612


Direction L1: >>          Initial region span: 1-463,464-466,467-469Gap history (edge excluded): 463-467 ->  


Alt. candidates: [], []                                                                                                    


Model 1BP/2BP comparison: 2BP vs 1BP: 4.70e-03                                                                             


Rec. model vs L1: 1.28e-02Rec. model vs L2: 0.00e+00                                                                


Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 463 49.059057 None None None * * *
|||||

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 466 3.420355 NaN NaN NaN * * *
A.1 995 464 -0.710160 -1.941794 9.883589 4.700906e-03 *
A.1.NmC2 83 464 -10.000000 -19.755055 45.510109 8.614407e-11
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 467 0.705991 None None None * * *



Target sequence

, 206_G|A, 212_C|T, 233_G|A, 254_A|G, 257_T|A, 266_T|C, 320_A|C, 419_A|T, 428_T|C, 431_T|C, 467_T|C, 475_C|T, 485_T|C, 515_G|A, 523_A|G, 534_G|A, 558_T|C, 564_A|G, 578_T|C, 617_C|A, 639_C|T,
653_G|A, 674_T|C, 689_G|A, 692_A|G, 734_A|G, 770_C|T, 803_A|G, 842_T|C, 878_C|T, 884_A|G, 899_C|T, 957_C|T, 977_C|T, 1007_C|T, 1034_T|C, 1070_C|T, 1091_A|G, 1094_G|A, 1100_C|T, 1103_C|T,
1110_C|T, 1115_T|C, 1124_A|G, 1127_C|T, 1160_T|C, 1175_A|G, 1232_A|G, 1250_C|T, 1277_C|T, 1298_T|C, 1328_T|C, 1355_C|T, 1379_T|C, 1433_C|T, 1444_C|T, 1520_G|A, 1607_C|T, 1616_C|G, 1634_C|T,
1644_T|C, 1655_C|T, 1682_C|T, 1701_C|T, 1769_A|C, 1781_C|T, 1793_T|C, 1854_C|T, 1865_T|C, 1898_G|A, 1907_A|G, 1940_A|G, 1946_C|T, 1973_C|T, 1991_T|C, 2021_C|T, 2066_C|T, 2069_A|G, 2090_C|T,
2093_T|A, 2103_C|T, 2114_T|C, 2129_C|T, 2150_C|T, 2156_G|T, 2198_T|C, 2228_T|C, 2279_T|C, 2285_C|T, 2381_T|A, 2394_A|G, 2437_T|C, 2469_T|C, 2474_C|T, 2501_C|T, 2525_G|A, 2540_A|G, 2606_C|T,
2633_A|G, 2648_T|G, 2654_C|T, 2681_G|A, 2687_C|T, 2723_CT|TC, 2792_A|G, 2798_A|G, 2804_C|T, 2816_C|T, 2831_C|T, 2840_T|C, 2858_C|T, 2864_A|G, 2876_A|C, 2879_T|C, 2891_C|T, 2921_A|G, 2925_G|A,
2930_T|C, 2963_T|C, 2996_C|T, 2999_G|A, 3002_T|C, 3008_A|G, 3014_T|C, 3038_T|C, 3041_T|A, 3052_T|C, 3059_G|A, 3068_T|C, 3071_A|G, 3104_G|A, 3110_T|C, 3134_C|T, 3137_T|C, 3140_A|G, 3180_T|C,
3186_G|A, 3203_G|A, 3218_T|A, 3221_C|T, 3248_T|C, 3254_T|C, 3275_C|T, 3279_A|G, 3290_A|G, 3296_C|T, 3314_T|C, 3329_C|T, 3332_G|A, 3338_T|C, 3368_A|G, 3377_A|G, 3380_T|C, 3434_G|A, 3450_C|T,
3464_T|A, 3506_A|G, 3515_A|G, 3518_C|T, 3522_T|C, 3534_G|A, 3666_C|T, 3705_C|T, 3723_T|C, 3731_C|T, 3806_A|C, 3818_A|C, 3836_T|C, 3854_A|G, 3881_T|C, 3885_T|C, 3895_C|T, 3906_T|C, 3973_T|C,
3989_T|C, 4034_G|A, 4049_G|A, 4076_C|T, 4085_T|C, 4106_A|G, 4112_C|T, 4128_T|C, 4146_C|T, 4172_C|T, 4238_C|T, 4268_C|T, 4272_T|C, 4277_T|C, 4292_G|A, 4322_C|T, 4325_G|A, 4328_C|T, 4331_T|C,
4343_C|T, 4424_C|T, 4436_T|C, 4454_G|A, 4493_C|T, 4589_C|T, 4592_A|G, 4595_C|T, 4610_A|G, 4682_C|T, 4688_A|G, 4697_T|C, 4733_T|C, 4751_T|C, 4790_A|G, 4829_C|T, 4856_T|C, 4859_A|G, 4877_C|T,
4886_G|A, 4904_C|T, 4961_T|C, 4982_T|C, 4988_G|A, 4994_G|T, 5000_T|C, 5027_A|G, 5060_T|C, 5090_G|A, 5144_G|A, 5153_G|A, 5189_A|G, 5192_CT|TC, 5267_T|C, 5270_T|G, 5277_T|C, 5279_A|G, 5342_T|C,
5357_C|T, 5375_A|G, 5387_C|T, 5390_C|T, 5420_T|C, 5429_G|A, 5432_A|C, 5435_C|T, 5450_T|C, 5456_G|T, 5459_T|C, 5516_T|A, 5567_G|A, 5582_T|C, 5600_C|T, 5612_T|C, 5621_C|A, 5723_T|C, 5732_A|G,
5747_G|A, 5811_C|A, 5828_T|C, 5834_G|A, 5846_T|C, 5867_T|C, 5879_T|G, 5903_A|G, 5937_T|C, 6027_C|A, 6056_C|T, 6092_C|T, 6098_C|T, 6101_T|C, 6152_C|T, 6155_A|G, 6299_C|T, 6363_C|T, 6443_G|A,
6446_G|A, 6473_T|C, 6524_A|G, 6527_C|T, 6584_T|C, 6608_G|A, 6618_C|T, 6629_T|C, 6641_G|T, 6671_T|C, 6674_C|T, 6684_A|C, 6725_T|C, 6737_C|T, 6746_C|T, 6797_T|C, 6803_C|T, 6842_A|G, 6872_C|T,
6890_A|G, 6908_T|A, 6944_G|A, 6954_A|G, 6983_A|G, 6992_A|G, 7014_C|T, 7037_C|T, 7046_T|C, 7049_CT|TC, 7059_T|C, 7064_T|C, 7085_A|G, 7088_G|A, 7136_T|C, 7151_T|C, 7175_C|T, 7178_A|G, 7187_T|C,
7208_A|G, 7233_C|T, 7239_C|T, 7257_T|C, 7292_G|T, 7295_G|A, 7307_T|G, 7313_T|C, 7430_G|A, 7451_AG|CA, 7460_C|T, 7464_A|G, 7466_A|T, 7470_TC|CT, 7475_G|C, 7550_C|T, 7553_G|A, 7568_T|C,
7625_A|T, 7628_C|T, 7633_T|C, 7653_T|C, 7670_G|A, 7679_A|G, 7694_A|G, 7713_T|C, 7739_C|T, 7769_G|A, 7784_G|A, 7805_T|C, 7808_T|A, 7817_G|A, 7844_T|C, 7853_G|T, 7869_C|A, 7871_G|A, 7964_A|G,
7982_A|G, 8007_GT|AC, 8027_G|A, 8069_T|C, 8078_T|G, 8082_C|T, 8093_G|T, 8159_C|A, 8198_A|G, 8213_A|G, 8237_T|C, 8252_G|A, 8353_C|T, 8393_G|A, 8408_T|C, 8450_T|C, 8459_G|A, 8467_T|C, 8477_T|C,
8490_A|C, 8511_A|G, 8516_A|G, 8534_C|T, 8555_C|T, 8570_T|C, 8591_A|G, 8597_T|C, 8606_C|T, 8624_C|T, 8630_A|C, 8660_A|G, 8720_T|C, 8771_A|G, 8789_T|G, 8794_G|A, 8811_T|C, 8813_G|A, 8819_A|G,
8828_C|T, 8849_C|T, 8852_T|C, 8873_C|T, 8882_T|C, 8895_T|C, 8897_A|G, 8918_A|G, 8924_G|A, 8969_T|C, 8997_C|T, 9011_C|T, 9017_T|C, 9053_A|G, 9092_C|T, 9098_T|C, 9128_C|T, 9176_C|T, 9215_C|T,
9224_C|T, 9233_G|A, 9239_T|C, 9244_T|C, 9256_G|A, 9272_C|T, 9275_T|C, 9299_C|T, 9305_C|T, 9326_A|G, 9353_T|C, 9365_A|G, 9427_A|G, 9434_A|G, 9449_T|C, 9452_T|C, 9455_G|A, 9470_G|A, 9488_C|T,
9503_C|T, 9509_T|C, 9518_A|G, 9527_A|G, 9539_T|C, 9582_C|T, 9585_C|A, 9591_T|C, 9599_A|G, 9607_A|G, 9668_C|T, 9677_G|A, 9713_C|T, 9722_T|C, 9728_A|G, 9749_A|G, 9774_GA|AG, 9804_C|T, 9806_C|T,
9821_CC|TT, 9824_T|C, 9851_T|C, 9857_C|T, 9884_G|A, 9896_T|A, 9950_G|A, 9965_C|T, 10004_T|C, 10052_T|C, 10094_A|G, 10148_A|G, 10163_T|C, 10208_G|A, 10223_C|T, 10238_G|A, 10244_C|T, 10247_C|T,
10266_A|G, 10331_C|T, 10361_T|C, 10374_C|T, 10376_G|A, 10388_C|T, 10392_A|G, 10477_T|C, 10561_T|C, 10612_T|C, 10654_A|G, 10666_T|C
 Case 3 (A.1): KX601167.1




Target: 995 samples       Number of changes: 466                                                                    


BC: A.1 + A.1.NmC1 + A.1  BC BR: 460-461, 463-464                   BC BR coord: 10391 - 10392, 10611 - 10612


Direction L1: >>          Initial region span: 1-460,461-463,464-466Gap history (edge excluded): 460-464 ->  


Alt. candidates: [], []                                                                                                    


Model 1BP/2BP comparison: 2BP vs 1BP: 4.70e-03                                                                             


Rec. model vs L1: 1.28e-02Rec. model vs L2: 0.00e+00                                                                


Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 460 48.181794 None None None * * *
|||||

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 463 3.420355 NaN NaN NaN * * *
A.1 995 461 -0.710160 -1.941794 9.883589 4.700906e-03 *
A.1.NmC2 83 461 -10.000000 -19.755055 45.510109 8.614407e-11
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 464 0.705991 None None None * * *



Target sequence

, 206_G|A, 212_C|T, 233_G|A, 254_A|G, 257_T|A, 266_T|C, 320_A|C, 419_A|T, 428_T|C, 431_T|C, 467_T|C, 475_C|T, 485_T|C, 515_G|A, 523_A|G, 558_T|C, 564_A|G, 578_T|C, 617_C|A, 639_C|T, 653_G|A,
674_T|C, 689_G|A, 692_A|G, 734_A|G, 770_C|T, 803_A|G, 842_T|C, 878_C|T, 884_A|G, 899_C|T, 957_C|T, 977_C|T, 1007_C|T, 1034_T|C, 1070_C|T, 1091_A|G, 1094_G|A, 1100_C|T, 1103_C|T, 1110_C|T,
1115_T|C, 1124_A|G, 1127_C|T, 1160_T|C, 1175_A|G, 1232_A|G, 1250_C|T, 1277_C|T, 1298_T|C, 1328_T|C, 1355_C|T, 1379_T|C, 1433_C|T, 1520_G|A, 1607_C|T, 1616_C|G, 1634_C|T, 1644_T|C, 1655_C|T,
1682_C|T, 1701_C|T, 1769_A|C, 1781_C|T, 1793_T|C, 1854_C|T, 1865_T|C, 1898_G|A, 1907_A|G, 1940_A|G, 1946_C|T, 1973_C|T, 1991_T|C, 2021_C|T, 2066_C|T, 2069_A|G, 2090_C|T, 2093_T|A, 2103_C|T,
2114_T|C, 2129_C|T, 2150_C|T, 2156_G|T, 2178_C|T, 2198_T|C, 2228_T|C, 2279_T|C, 2285_C|T, 2381_T|A, 2394_A|G, 2437_T|C, 2469_T|C, 2474_C|T, 2501_C|T, 2525_G|A, 2540_A|G, 2606_C|T, 2633_A|G,
2648_T|G, 2654_C|T, 2681_G|A, 2687_C|T, 2723_CT|TC, 2792_A|G, 2798_A|G, 2804_C|T, 2816_C|T, 2831_C|T, 2840_T|C, 2858_C|T, 2864_A|G, 2876_A|C, 2879_T|C, 2891_C|T, 2921_A|G, 2925_G|A, 2930_T|C,
2963_T|C, 2996_C|T, 2999_G|A, 3002_T|C, 3008_A|G, 3014_T|C, 3038_T|C, 3041_T|A, 3052_T|C, 3059_G|A, 3068_T|C, 3071_A|G, 3104_G|A, 3110_T|C, 3134_C|T, 3137_T|C, 3140_A|G, 3180_T|C, 3186_G|A,
3203_G|A, 3218_T|A, 3221_C|T, 3248_T|C, 3254_T|C, 3275_C|T, 3279_A|G, 3290_A|G, 3296_C|T, 3314_T|C, 3329_C|T, 3332_G|A, 3338_T|C, 3368_A|G, 3377_A|G, 3380_T|C, 3434_G|A, 3450_C|T, 3464_T|A,
3506_A|G, 3515_A|G, 3518_C|T, 3522_T|C, 3534_G|A, 3666_C|T, 3705_C|T, 3723_T|C, 3731_C|T, 3806_A|C, 3818_A|C, 3836_T|C, 3854_A|G, 3881_T|C, 3885_T|C, 3906_T|C, 3973_T|C, 3989_T|C, 4034_G|A,
4049_G|A, 4076_C|T, 4085_T|C, 4106_A|G, 4112_C|T, 4128_T|C, 4146_C|T, 4172_C|T, 4238_C|T, 4268_C|T, 4272_T|C, 4277_T|C, 4292_G|A, 4322_C|T, 4325_G|A, 4328_C|T, 4331_T|C, 4343_C|T, 4424_C|T,
4436_T|C, 4454_G|A, 4493_C|T, 4589_C|T, 4592_A|G, 4595_C|T, 4610_A|G, 4682_C|T, 4688_A|G, 4697_T|C, 4733_T|C, 4751_T|C, 4790_A|G, 4829_C|T, 4856_T|C, 4859_A|G, 4877_C|T, 4886_G|A, 4904_C|T,
4961_T|C, 4982_T|C, 4988_G|A, 4994_G|T, 5000_T|C, 5027_A|G, 5060_T|C, 5090_G|A, 5144_G|A, 5153_G|A, 5189_A|G, 5192_CT|TC, 5267_T|C, 5270_T|G, 5277_T|C, 5279_A|G, 5342_T|C, 5357_C|T, 5375_A|G,
5387_C|T, 5390_C|T, 5420_T|C, 5429_G|A, 5432_A|C, 5435_C|T, 5450_T|C, 5456_G|T, 5459_T|C, 5516_T|A, 5567_G|A, 5582_T|C, 5600_C|T, 5612_T|C, 5621_C|A, 5723_T|C, 5732_A|G, 5747_G|A, 5811_C|A,
5828_T|C, 5834_G|A, 5846_T|C, 5867_T|C, 5879_T|G, 5903_A|G, 5937_T|C, 6027_C|A, 6056_C|T, 6092_C|T, 6098_C|T, 6101_T|C, 6152_C|T, 6155_A|G, 6299_C|T, 6363_C|T, 6443_G|A, 6446_G|A, 6473_T|C,
6524_A|G, 6527_C|T, 6584_T|C, 6608_G|A, 6618_C|T, 6629_T|C, 6641_G|T, 6671_T|C, 6674_C|T, 6684_A|C, 6725_T|C, 6737_C|T, 6746_C|T, 6797_T|C, 6803_C|T, 6842_A|G, 6872_C|T, 6890_A|G, 6908_T|A,
6944_G|A, 6954_A|G, 6983_A|G, 6992_A|G, 7014_C|T, 7037_C|T, 7046_T|C, 7049_CT|TC, 7059_T|C, 7064_T|C, 7085_A|G, 7088_G|A, 7136_T|C, 7151_T|C, 7175_C|T, 7178_A|G, 7187_T|C, 7208_A|G, 7233_C|T,
7239_C|T, 7257_T|C, 7292_G|T, 7295_G|A, 7307_T|G, 7313_T|C, 7430_G|A, 7451_AG|CA, 7460_C|T, 7464_A|G, 7466_A|T, 7470_TC|CT, 7475_G|C, 7550_C|T, 7553_G|A, 7568_T|C, 7625_A|T, 7628_C|T,
7633_T|C, 7653_T|C, 7670_G|A, 7679_A|G, 7694_A|G, 7713_T|C, 7739_C|T, 7769_G|A, 7784_G|A, 7805_T|C, 7808_T|A, 7817_G|A, 7844_T|C, 7853_G|T, 7869_C|A, 7871_G|A, 7964_A|G, 7982_A|G, 8007_GT|AC,
8027_G|A, 8069_T|C, 8078_T|G, 8082_C|T, 8093_G|T, 8159_C|A, 8198_A|G, 8213_A|G, 8237_T|C, 8252_G|A, 8353_C|T, 8393_G|A, 8408_T|C, 8450_T|C, 8459_G|A, 8467_T|C, 8477_T|C, 8490_A|C, 8511_A|G,
8516_A|G, 8534_C|T, 8555_C|T, 8570_T|C, 8591_A|G, 8597_T|C, 8606_C|T, 8624_C|T, 8630_A|C, 8660_A|G, 8720_T|C, 8771_A|G, 8789_T|G, 8794_G|A, 8811_T|C, 8813_G|A, 8819_A|G, 8828_C|T, 8849_C|T,
8852_T|C, 8873_C|T, 8882_T|C, 8895_T|C, 8897_A|G, 8918_A|G, 8924_G|A, 8969_T|C, 8997_C|T, 9011_C|T, 9017_T|C, 9053_A|G, 9092_C|T, 9098_T|C, 9128_C|T, 9176_C|T, 9215_C|T, 9224_C|T, 9233_G|A,
9239_T|C, 9244_T|C, 9256_G|A, 9272_C|T, 9275_T|C, 9299_C|T, 9305_C|T, 9326_A|G, 9353_T|C, 9365_A|G, 9427_A|G, 9434_A|G, 9449_T|C, 9452_T|C, 9455_G|A, 9470_G|A, 9488_C|T, 9503_C|T, 9509_T|C,
9518_A|G, 9527_A|G, 9539_T|C, 9582_C|T, 9585_C|A, 9591_T|C, 9599_A|G, 9607_A|G, 9668_C|T, 9677_G|A, 9713_C|T, 9722_T|C, 9728_A|G, 9749_A|G, 9774_GA|AG, 9806_C|T, 9821_CC|TT, 9824_T|C,
9851_T|C, 9857_C|T, 9884_G|A, 9896_T|A, 9950_G|A, 9965_C|T, 10004_T|C, 10052_T|C, 10094_A|G, 10148_A|G, 10163_T|C, 10208_G|A, 10223_C|T, 10238_G|A, 10244_C|T, 10247_C|T, 10266_A|G, 10331_C|T,
10361_T|C, 10374_C|T, 10376_G|A, 10388_C|T, 10392_A|G, 10477_T|C, 10561_T|C, 10612_T|C, 10654_A|G, 10666_T|C
 Case 3 (A.1): KX694533.2




Target: 995 samples       Number of changes: 469                                                                    


BC: A.1 + A.1.NmC1 + A.1  BC BR: 463-464, 466-467                   BC BR coord: 10391 - 10392, 10611 - 10612


Direction L1: >>          Initial region span: 1-463,464-466,467-469Gap history (edge excluded): 463-467 ->  


Alt. candidates: [], []                                                                                                    


Model 1BP/2BP comparison: 2BP vs 1BP: 4.70e-03                                                                             


Rec. model vs L1: 1.27e-02Rec. model vs L2: 0.00e+00                                                                


Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 463 48.965966 None None None * * *
|||||

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 466 3.420355 NaN NaN NaN * * *
A.1 995 464 -0.710160 -1.941794 9.883589 4.700906e-03 *
A.1.NmC2 83 464 -10.000000 -19.755055 45.510109 8.614407e-11
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 467 0.705991 None None None * * *



Target sequence

, 56_G|A, 206_G|A, 212_C|T, 233_G|A, 254_A|G, 257_T|A, 266_T|C, 320_A|C, 419_A|T, 428_T|C, 431_T|C, 467_T|C, 475_C|T, 485_T|C, 515_G|A, 523_A|G, 534_G|A, 558_T|C, 564_A|G, 578_T|C, 617_C|A,
639_C|T, 653_G|A, 674_T|C, 689_G|A, 692_A|G, 734_A|G, 770_C|T, 803_A|G, 842_T|C, 878_C|T, 884_A|G, 899_C|T, 957_C|T, 977_C|T, 1007_C|T, 1034_T|C, 1070_C|T, 1091_A|G, 1094_G|A, 1100_C|T,
1103_C|T, 1110_C|T, 1115_T|C, 1124_A|G, 1127_C|T, 1160_T|C, 1175_A|G, 1232_A|G, 1250_C|T, 1277_C|T, 1298_T|C, 1328_T|C, 1355_C|T, 1379_T|C, 1433_C|T, 1444_C|T, 1520_G|A, 1607_C|T, 1616_C|G,
1634_C|T, 1644_T|C, 1655_C|T, 1682_C|T, 1701_C|T, 1769_A|C, 1781_C|T, 1793_T|C, 1854_C|T, 1865_T|C, 1898_G|A, 1907_A|G, 1940_A|G, 1946_C|T, 1973_C|T, 1991_T|C, 2021_C|T, 2066_C|T, 2069_A|G,
2090_C|T, 2093_T|A, 2103_C|T, 2114_T|C, 2129_C|T, 2150_C|T, 2156_G|T, 2198_T|C, 2228_T|C, 2279_T|C, 2285_C|T, 2381_T|A, 2394_A|G, 2437_T|C, 2469_T|C, 2474_C|T, 2501_C|T, 2525_G|A, 2540_A|G,
2606_C|T, 2633_A|G, 2648_T|G, 2654_C|T, 2681_G|A, 2687_C|T, 2723_CT|TC, 2792_A|G, 2798_A|G, 2804_C|T, 2816_C|T, 2831_C|T, 2840_T|C, 2858_C|T, 2864_A|G, 2876_A|C, 2879_T|C, 2891_C|T, 2921_A|G,
2925_G|A, 2930_T|C, 2963_T|C, 2996_C|T, 2999_G|A, 3002_T|C, 3008_A|G, 3014_T|C, 3038_T|C, 3041_T|A, 3052_T|C, 3059_G|A, 3068_T|C, 3071_A|G, 3104_G|A, 3110_T|C, 3134_C|T, 3137_T|C, 3140_A|G,
3180_T|C, 3186_G|A, 3203_G|A, 3218_T|A, 3221_C|T, 3248_T|C, 3254_T|C, 3275_C|T, 3279_A|G, 3290_A|G, 3296_C|T, 3314_T|C, 3329_C|T, 3332_G|A, 3338_T|C, 3368_A|G, 3377_A|G, 3380_T|C, 3434_G|A,
3450_C|T, 3464_T|A, 3506_A|G, 3515_A|G, 3518_C|T, 3522_T|C, 3534_G|A, 3666_C|T, 3705_C|T, 3723_T|C, 3731_C|T, 3806_A|C, 3818_A|C, 3836_T|C, 3854_A|G, 3881_T|C, 3885_T|C, 3895_C|T, 3906_T|C,
3973_T|C, 3989_T|C, 4034_G|A, 4049_G|A, 4076_C|T, 4085_T|C, 4106_A|G, 4112_C|T, 4128_T|C, 4146_C|T, 4172_C|T, 4238_C|T, 4268_C|T, 4272_T|C, 4277_T|C, 4292_G|A, 4322_C|T, 4325_G|A, 4328_C|T,
4331_T|C, 4343_C|T, 4424_C|T, 4436_T|C, 4454_G|A, 4493_C|T, 4589_C|T, 4592_A|G, 4595_C|T, 4610_A|G, 4682_C|T, 4688_A|G, 4697_T|C, 4733_T|C, 4751_T|C, 4790_A|G, 4829_C|T, 4856_T|C, 4859_A|G,
4877_C|T, 4886_G|A, 4904_C|T, 4961_T|C, 4982_T|C, 4988_G|A, 4994_G|T, 5000_T|C, 5027_A|G, 5060_T|C, 5090_G|A, 5144_G|A, 5153_G|A, 5189_A|G, 5192_CT|TC, 5267_T|C, 5270_T|G, 5277_T|C, 5279_A|G,
5342_T|C, 5357_C|T, 5375_A|G, 5387_C|T, 5390_C|T, 5420_T|C, 5429_G|A, 5432_A|C, 5435_C|T, 5450_T|C, 5456_G|T, 5459_T|C, 5516_T|A, 5567_G|A, 5582_T|C, 5600_C|T, 5612_T|C, 5621_C|A, 5723_T|C,
5732_A|G, 5747_G|A, 5811_C|A, 5828_T|C, 5834_G|A, 5846_T|C, 5867_T|C, 5879_T|G, 5903_A|G, 5937_T|C, 6027_C|A, 6056_C|T, 6092_C|T, 6098_C|T, 6101_T|C, 6152_C|T, 6155_A|G, 6299_C|T, 6363_C|T,
6443_G|A, 6446_G|A, 6473_T|C, 6524_A|G, 6527_C|T, 6584_T|C, 6608_G|A, 6618_C|T, 6629_T|C, 6641_G|T, 6671_T|C, 6674_C|T, 6684_A|C, 6725_T|C, 6737_C|T, 6746_C|T, 6797_T|C, 6803_C|T, 6842_A|G,
6872_C|T, 6890_A|G, 6908_T|A, 6944_G|A, 6954_A|G, 6983_A|G, 6992_A|G, 7014_C|T, 7037_C|T, 7046_T|C, 7049_CT|TC, 7059_T|C, 7064_T|C, 7085_A|G, 7088_G|A, 7136_T|C, 7151_T|C, 7175_C|T, 7178_A|G,
7187_T|C, 7208_A|G, 7233_C|T, 7239_C|T, 7257_T|C, 7292_G|T, 7295_G|A, 7307_T|G, 7313_T|C, 7430_G|A, 7451_AG|CA, 7460_C|T, 7464_A|G, 7466_A|T, 7470_TC|CT, 7475_G|C, 7550_C|T, 7553_G|A,
7568_T|C, 7625_A|T, 7628_C|T, 7633_T|C, 7653_T|C, 7670_G|A, 7679_A|G, 7694_A|G, 7713_T|C, 7739_C|T, 7769_G|A, 7784_G|A, 7805_T|C, 7808_T|A, 7817_G|A, 7844_T|C, 7853_G|T, 7869_C|A, 7871_G|A,
7964_A|G, 7982_A|G, 8007_GT|AC, 8027_G|A, 8069_T|C, 8078_T|G, 8082_C|T, 8093_G|T, 8159_C|A, 8198_A|G, 8213_A|G, 8237_T|C, 8252_G|A, 8353_C|T, 8393_G|A, 8408_T|C, 8450_T|C, 8459_G|A, 8467_T|C,
8477_T|C, 8490_A|C, 8511_A|G, 8516_A|G, 8534_C|T, 8555_C|T, 8570_T|C, 8591_A|G, 8597_T|C, 8606_C|T, 8624_C|T, 8630_A|C, 8660_A|G, 8720_T|C, 8771_A|G, 8789_T|G, 8794_G|A, 8811_T|C, 8813_G|A,
8819_A|G, 8828_C|T, 8849_C|T, 8852_T|C, 8873_C|T, 8882_T|C, 8895_T|C, 8897_A|G, 8918_A|G, 8924_G|A, 8969_T|C, 8997_C|T, 9011_C|T, 9017_T|C, 9053_A|G, 9092_C|T, 9098_T|C, 9128_C|T, 9176_C|T,
9215_C|T, 9224_C|T, 9233_G|A, 9239_T|C, 9244_T|C, 9256_G|A, 9272_C|T, 9275_T|C, 9299_C|T, 9305_C|T, 9326_A|G, 9353_T|C, 9365_A|G, 9427_A|G, 9434_A|G, 9449_T|C, 9452_T|C, 9455_G|A, 9470_G|A,
9488_C|T, 9503_C|T, 9509_T|C, 9518_A|G, 9527_A|G, 9539_T|C, 9582_C|T, 9585_C|A, 9591_T|C, 9599_A|G, 9607_A|G, 9668_C|T, 9677_G|A, 9713_C|T, 9722_T|C, 9728_A|G, 9749_A|G, 9774_GA|AG, 9806_C|T,
9821_CC|TT, 9824_T|C, 9851_T|C, 9857_C|T, 9884_G|A, 9896_T|A, 9950_G|A, 9965_C|T, 10004_T|C, 10052_T|C, 10094_A|G, 10148_A|G, 10163_T|C, 10208_G|A, 10223_C|T, 10238_G|A, 10244_C|T, 10247_C|T,
10266_A|G, 10331_C|T, 10361_T|C, 10374_C|T, 10376_G|A, 10388_C|T, 10392_A|G, 10477_T|C, 10561_T|C, 10612_T|C, 10654_A|G, 10666_T|C
 Case 3 (A.1): MG645981.1




Target: 995 samples       Number of changes: 148                                                                  


BC: A.1 + A.1.NmC1 + A.1  BC BR: 81-82, 84-85                   BC BR coord: 5287 - 5288, 5560 - 5561      


Direction L1: >>          Initial region span: 1-10,83-84,85-148Gap history (edge excluded): 10-85 -> 10-83


Alt. candidates: [], []                                                                                                  


Model 1BP/2BP comparison: 2BP vs 1BP: 4.09e-13                                                                           


Rec. model vs L1: 6.38e+01Rec. model vs L2: 0.00e+00                                                              


Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 10 1.974196 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 83 3.012208 NaN NaN NaN * * *
A.1 995 84 -0.964789 -1.418915 10.83783 2.138276e+00 * *
A.1.NmC2 83 84 -10.000000 -30.000000 68.00000 8.278040e-13 *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 85 1.692512 None None None * * *



Target sequence

, 102_C|T, 122_A|G, 130_C|T, 164_C|G, 216_C|T, 254_A|G, 423_G|A, 467_T|C, 475_C|T, 523_AC|GT, 558_T|C, 653_G|A, 718_AT|GC, 803_A|G, 1070_C|T, 1175_A|G, 1343_C|T, 1481_G|C, 1535_A|T, 1577_T|C,
1616_C|T, 1621_A|G, 1655_C|T, 1908_G|T, 1922_C|T, 2066_C|T, 2285_C|T, 2375_C|T, 2394_A|G, 2411_C|T, 2525_G|A, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3038_T|C, 3050_T|C,
3052_T|C, 3059_G|A, 3071_A|G, 3110_T|C, 3137_T|C, 3140_A|G, 3167_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3282_A|G, 3332_G|A, 3473_C|T, 3518_C|T, 3534_G|A, 3731_C|T, 3806_A|T, 3854_A|G,
3885_T|C, 3989_T|C, 4085_T|C, 4106_A|G, 4108_A|G, 4238_C|T, 4295_A|G, 4454_G|A, 4481_G|A, 4493_C|T, 4523_G|A, 4536_A|G, 4592_A|G, 4595_C|T, 4697_T|C, 4733_T|C, 4751_T|C, 4988_G|A, 5000_T|C,
5036_C|T, 5060_T|C, 5066_C|T, 5213_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5561_C|T, 5591_T|C, 5825_C|A, 5828_T|C, 5937_T|C, 6056_C|T, 6092_C|T, 6101_T|C, 6164_C|T, 6363_CA|TG, 6443_G|A, 6473_T|C,
6533_A|G, 6584_T|C, 6629_T|C, 6684_A|C, 6746_C|T, 6890_A|G, 6983_A|G, 7037_C|T, 7049_CT|TC, 7157_C|T, 7319_C|T, 7451_A|C, 7517_C|T, 7568_T|C, 7633_T|C, 7679_A|G, 7700_A|G, 7713_T|C, 7805_T|C,
7869_C|A, 8000_A|G, 8007_G|A, 8105_C|T, 8408_T|C, 8516_A|G, 8597_T|C, 9017_T|C, 9098_T|C, 9176_C|T, 9225_C|T, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9503_C|T, 9527_A|G, 9623_C|T, 9673_T|G,
9677_G|A, 9704_C|T, 9815_C|T, 9884_G|A, 9896_T|A, 10217_A|G, 10281_G|A, 10361_T|C, 10376_G|A, 10386_A|G, 10392_A|G, 10477_T|C, 10561_T|C, 10685_G|C
 Case 3 (A.1): MH158236.1




Target: 995 samples        Number of changes: 176                                               


BC: A.1 + A.1.NmC1         BC BR: 172-173                    BC BR coord: 10391 - 10392  


Direction L1: >>           Initial region span: 1-172,173-176Gap history (edge excluded):


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison:  -                                                                           


Rec. model vs L1: 6.96e-02 Rec. model vs L2: 0.00e+00                                           


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 172 3.70039 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 173 3.420355 None None None * * *



Target sequence

, 122_A|G, 254_A|G, 359_C|T, 423_G|A, 467_T|C, 475_C|T, 496_G|A, 523_A|G, 558_T|A, 653_G|A, 719_T|C, 803_A|G, 837_T|C, 1070_C|T, 1175_A|G, 1337_A|T, 1343_C|T, 1442_C|T, 1616_C|T, 1655_C|T,
1736_A|G, 1922_C|T, 2066_C|T, 2093_T|C, 2111_T|G, 2156_G|A, 2282_A|G, 2285_C|T, 2298_T|C, 2375_C|T, 2394_A|G, 2411_C|T, 2525_G|A, 2570_C|T, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C,
2828_C|T, 2864_A|G, 2925_G|A, 3038_T|C, 3050_T|C, 3052_T|C, 3059_G|A, 3071_A|G, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3296_C|T, 3332_G|A, 3473_C|T, 3518_C|T,
3534_G|A, 3605_G|A, 3617_G|A, 3731_C|T, 3767_A|T, 3806_A|T, 3827_C|T, 3854_A|G, 3885_T|C, 3928_T|C, 3989_T|C, 4085_T|C, 4094_C|T, 4106_A|G, 4238_C|T, 4295_A|G, 4454_G|A, 4481_G|A, 4493_C|T,
4523_G|A, 4536_A|G, 4592_A|G, 4595_C|T, 4733_T|C, 4751_T|C, 4988_G|A, 5000_T|C, 5036_C|T, 5060_T|C, 5066_C|T, 5096_T|C, 5267_T|C, 5369_C|T, 5375_A|G, 5387_C|T, 5561_C|T, 5591_T|C, 5717_C|T,
5828_T|C, 5937_T|C, 6002_T|C, 6056_C|T, 6092_C|T, 6101_T|C, 6164_C|T, 6363_C|T, 6443_G|A, 6473_T|C, 6512_C|T, 6533_A|G, 6584_T|C, 6608_G|A, 6626_C|T, 6629_T|C, 6684_A|C, 6746_C|T, 6890_A|G,
6983_A|G, 6989_C|T, 7037_C|T, 7049_CT|TC, 7148_T|C, 7157_C|T, 7175_C|T, 7451_A|T, 7493_G|T, 7517_C|T, 7538_A|G, 7568_T|C, 7577_T|C, 7604_T|C, 7633_T|C, 7679_A|G, 7713_T|C, 7805_T|C, 7826_T|C,
7869_C|A, 7937_C|T, 8007_G|A, 8105_C|T, 8387_C|T, 8408_T|C, 8429_G|A, 8516_A|G, 8597_T|C, 8823_C|T, 8888_T|C, 9017_T|C, 9098_T|C, 9176_C|T, 9200_G|A, 9225_C|T, 9272_C|T, 9305_C|T, 9353_T|C,
9434_A|G, 9455_G|A, 9503_C|T, 9527_A|G, 9623_C|T, 9677_G|A, 9704_C|T, 9758_A|G, 9884_G|A, 9887_C|T, 9896_T|A, 9899_A|G, 10217_A|G, 10281_G|A, 10286_C|T, 10314_A|G, 10349_T|C, 10361_T|C,
10376_G|A, 10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): MT377502.1




Target: 995 samples        Number of changes: 142                                                   


BC: A.1 + A.1.NmC1         BC BR: 136-137                  BC BR coord: 10288 - 10289        


Direction L1: <<           Initial region span: 1-6,140-142Gap history (edge excluded): 6-140


Alt. candidates: [], []                                                                                    


Model 1BP/2BP comparison:  -                                                                               


Rec. model vs L1: 2.93e+15 Rec. model vs L2: 0.00e+00                                               


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 1.032875 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 140 3.420355 None None None * * *



Target sequence

, 122_A|G, 254_A|G, 423_G|A, 467_T|C, 475_C|T, 523_AC|GT, 558_T|C, 653_G|A, 719_T|C, 803_A|G, 1070_C|T, 1175_A|G, 1241_T|C, 1343_C|T, 1535_A|G, 1577_T|C, 1616_C|T, 1621_A|G, 1655_C|T,
1908_G|T, 1922_C|T, 2066_C|T, 2285_C|T, 2375_C|T, 2394_A|G, 2411_C|T, 2525_G|A, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3038_T|C, 3050_T|C, 3052_T|C, 3059_G|A, 3071_A|G,
3110_T|C, 3137_T|C, 3140_A|G, 3167_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3283_A|C, 3332_G|A, 3473_C|T, 3518_C|T, 3534_G|A, 3731_C|T, 3806_A|T, 3854_A|G, 3885_T|C, 3989_T|C, 4051_C|T,
4085_T|C, 4106_A|G, 4108_A|G, 4238_C|T, 4295_A|G, 4454_G|A, 4481_G|A, 4493_C|T, 4523_G|A, 4536_A|G, 4592_A|G, 4595_C|T, 4697_T|C, 4733_T|C, 4751_T|C, 4988_G|A, 5000_T|C, 5036_C|T, 5060_T|C,
5066_C|T, 5213_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5561_C|T, 5591_T|C, 5828_T|C, 5937_T|C, 6056_C|T, 6092_C|T, 6101_T|C, 6164_C|T, 6363_CA|TG, 6443_G|A, 6473_T|C, 6533_A|G, 6584_T|C, 6629_T|C,
6684_A|C, 6746_C|T, 6890_A|G, 6983_A|G, 7037_C|T, 7049_CT|TC, 7157_C|T, 7319_C|T, 7451_A|C, 7517_C|T, 7568_T|C, 7633_T|C, 7679_A|G, 7700_A|G, 7713_T|C, 7805_T|C, 7869_C|A, 8000_A|G, 8007_G|A,
8105_C|T, 8408_T|C, 8516_A|G, 8597_T|C, 9017_T|C, 9098_T|C, 9128_C|T, 9176_C|T, 9225_C|T, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9503_C|T, 9527_A|G, 9728_A|G, 9752_G|A, 9809_C|T, 9953_A|G,
10208_GT|AG, 10217_A|G, 10281_G|A, 10361_T|C, 10376_G|A, 10386_A|G, 10392_A|G, 10477_T|C, 10561_T|C
 Case 3 (A.1): MT377504.1




Target: 995 samples        Number of changes: 143                                                   


BC: A.1 + A.1.NmC1         BC BR: 137-138                  BC BR coord: 10288 - 10289        


Direction L1: <<           Initial region span: 1-6,141-143Gap history (edge excluded): 6-141


Alt. candidates: [], []                                                                                    


Model 1BP/2BP comparison:  -                                                                               


Rec. model vs L1: 2.93e+15 Rec. model vs L2: 0.00e+00                                               


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 1.032875 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 141 3.420355 NaN NaN NaN * * *
A.1 995 88 1.162314 -1.37812 16.756239 1.885738e+08 *



Target sequence

, 122_A|G, 254_A|G, 423_G|A, 467_T|C, 475_C|T, 523_AC|GT, 558_T|C, 653_G|A, 719_T|C, 803_A|G, 1070_C|T, 1175_A|G, 1343_C|T, 1535_A|G, 1577_T|C, 1616_C|T, 1621_A|G, 1655_C|T, 1908_G|T,
1922_C|T, 2066_C|T, 2285_C|T, 2298_T|C, 2305_A|G, 2375_C|T, 2394_A|G, 2411_C|T, 2525_G|A, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3038_T|C, 3050_T|C, 3052_T|C, 3059_G|A,
3071_A|G, 3110_T|C, 3137_T|C, 3140_A|G, 3167_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3283_A|C, 3332_G|A, 3473_C|T, 3518_C|T, 3534_G|A, 3731_C|T, 3806_A|T, 3854_A|G, 3885_T|C, 3989_T|C,
4051_C|T, 4085_T|C, 4106_A|G, 4108_A|G, 4238_C|T, 4295_A|G, 4454_G|A, 4481_G|A, 4493_C|T, 4523_G|A, 4536_A|G, 4592_A|G, 4595_C|T, 4697_T|C, 4733_T|C, 4751_T|C, 4988_G|A, 5000_T|C, 5036_C|T,
5060_T|C, 5066_C|T, 5213_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5561_C|T, 5591_T|C, 5828_T|C, 5937_T|C, 6056_C|T, 6092_C|T, 6101_T|C, 6164_C|T, 6363_CA|TG, 6443_G|A, 6473_T|C, 6533_A|G, 6584_T|C,
6629_T|C, 6684_A|C, 6746_C|T, 6890_A|G, 6983_A|G, 7037_C|T, 7049_CT|TC, 7157_C|T, 7319_C|T, 7451_A|C, 7517_C|T, 7568_T|C, 7633_T|C, 7679_A|G, 7700_A|G, 7713_T|C, 7805_T|C, 7869_C|A, 8000_A|G,
8007_G|A, 8105_C|T, 8408_T|C, 8516_A|G, 8597_T|C, 9017_T|C, 9098_T|C, 9176_C|T, 9225_C|T, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9503_C|T, 9527_A|G, 9623_C|T, 9677_G|A, 9704_C|T, 9815_C|T,
9884_G|A, 9896_T|A, 10217_A|G, 10281_G|A, 10361_T|C, 10376_G|A, 10386_A|G, 10392_A|G, 10477_T|C, 10561_T|C
 Case 3 (A.1): MW015936.1




Target: 995 samples        Number of changes: 142                                                   


BC: A.1 + A.1.NmC1         BC BR: 136-137                  BC BR coord: 10288 - 10289        


Direction L1: <<           Initial region span: 1-6,140-142Gap history (edge excluded): 6-140


Alt. candidates: [], []                                                                                    


Model 1BP/2BP comparison:  -                                                                               


Rec. model vs L1: 2.93e+15 Rec. model vs L2: 0.00e+00                                               


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 6 1.032875 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 140 3.420355 NaN NaN NaN * * *
A.1 995 127 0.840794 -1.37812 16.756239 1.885738e+08 *



Target sequence

, 122_A|G, 254_A|G, 423_G|A, 467_T|C, 475_C|T, 523_AC|GT, 558_T|C, 653_G|A, 719_T|C, 803_A|G, 1070_C|T, 1175_A|G, 1343_C|T, 1577_T|C, 1616_C|T, 1655_C|T, 1741_T|C, 1908_G|T, 1922_C|T,
2066_C|T, 2285_C|T, 2298_T|C, 2375_C|T, 2394_A|G, 2411_C|T, 2525_G|A, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3038_T|C, 3050_T|C, 3052_T|C, 3059_G|A, 3071_A|G, 3110_T|C,
3137_T|C, 3140_A|G, 3149_G|A, 3167_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3332_G|A, 3473_C|T, 3518_C|T, 3534_G|A, 3731_C|T, 3806_A|T, 3854_A|G, 3885_T|C, 3989_T|C, 4085_T|C, 4106_A|G,
4108_A|G, 4238_C|T, 4295_A|G, 4319_G|A, 4454_G|A, 4481_G|A, 4493_C|T, 4523_G|A, 4536_A|G, 4592_A|G, 4595_C|T, 4697_T|C, 4733_T|C, 4751_T|C, 4988_G|A, 5000_T|C, 5036_C|T, 5060_T|C, 5066_C|T,
5231_T|C, 5369_C|T, 5375_A|G, 5387_C|T, 5561_C|T, 5591_T|C, 5828_T|C, 5937_T|C, 6056_C|T, 6092_C|T, 6101_T|C, 6164_C|T, 6363_C|T, 6443_G|A, 6473_T|C, 6533_A|G, 6584_T|C, 6629_T|C, 6684_A|C,
6746_C|T, 6890_A|G, 6983_A|G, 7037_C|T, 7049_CT|TC, 7157_C|T, 7319_C|T, 7451_A|C, 7517_C|T, 7568_T|C, 7633_T|C, 7679_A|G, 7700_A|G, 7713_T|C, 7805_T|C, 7869_C|A, 8000_A|G, 8007_G|A, 8105_C|T,
8408_T|C, 8516_A|G, 8597_T|C, 9017_T|C, 9098_T|C, 9176_C|T, 9180_G|C, 9225_C|T, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9503_C|T, 9527_A|G, 9623_C|T, 9677_G|A, 9704_C|T, 9815_C|T, 9884_G|A,
9896_T|A, 10217_A|G, 10281_G|A, 10361_T|C, 10376_G|A, 10386_A|G, 10392_A|G, 10477_T|C, 10561_T|C
 Case 3 (A.1): OP281680.1




Target: 995 samples        Number of changes: 148                                                     


BC: A.1 + A.1.NmC1         BC BR: 142-143                   BC BR coord: 10288 - 10289         


Direction L1: <<           Initial region span: 1-12,146-148Gap history (edge excluded): 12-146


Alt. candidates: [], []                                                                                      


Model 1BP/2BP comparison:  -                                                                                 


Rec. model vs L1: 2.93e+15 Rec. model vs L2: 0.00e+00                                                 


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 12 2.444857 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 146 3.420355 NaN NaN NaN * * *
A.1 995 133 0.840794 -1.37812 16.756239 1.885738e+08 *



Target sequence

, 122_A|G, 127_A|G, 138_T|G, 145_T|G, 183_CC|TT, 187_T|A, 218_T|A, 254_A|G, 423_G|A, 467_T|C, 475_C|T, 523_AC|GT, 558_T|C, 653_G|A, 719_T|C, 803_A|G, 1070_C|T, 1175_A|G, 1343_C|T, 1577_T|C,
1616_C|T, 1655_C|T, 1908_G|T, 1922_C|T, 2066_C|T, 2285_C|T, 2298_T|C, 2375_C|T, 2394_A|G, 2411_C|T, 2525_G|A, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C, 2925_G|A, 3038_T|C, 3050_T|C,
3052_T|C, 3059_G|A, 3071_A|G, 3110_T|C, 3137_T|C, 3140_A|G, 3149_G|A, 3167_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3332_G|A, 3473_C|T, 3518_C|T, 3534_G|A, 3731_C|T, 3806_A|T, 3854_A|G,
3885_T|C, 3989_T|C, 4085_T|C, 4106_A|G, 4108_A|G, 4238_C|T, 4295_A|G, 4454_G|A, 4481_G|A, 4493_C|T, 4523_G|A, 4536_A|G, 4592_A|G, 4595_C|T, 4697_T|C, 4733_T|C, 4751_T|C, 4988_G|A, 5000_T|C,
5036_C|T, 5060_T|C, 5066_C|T, 5231_T|C, 5369_C|T, 5375_A|G, 5387_C|T, 5561_C|T, 5591_T|C, 5770_T|C, 5772_A|C, 5828_T|C, 5937_T|C, 6056_C|T, 6092_C|T, 6101_T|C, 6164_C|T, 6363_C|T, 6443_G|A,
6473_T|C, 6533_A|G, 6584_T|C, 6629_T|C, 6684_A|C, 6746_C|T, 6890_A|G, 6983_A|G, 7037_C|T, 7049_CT|TC, 7157_C|T, 7319_C|T, 7451_A|C, 7517_C|T, 7568_T|C, 7633_T|C, 7679_A|G, 7700_A|G, 7713_T|C,
7805_T|C, 7869_C|A, 8000_A|G, 8007_G|A, 8105_C|T, 8408_T|C, 8420_G|T, 8516_A|G, 8597_T|C, 9017_T|C, 9098_T|C, 9176_C|T, 9225_C|T, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9503_C|T, 9527_A|G,
9623_C|T, 9677_G|A, 9704_C|T, 9815_C|T, 9884_G|A, 9896_T|A, 10217_A|G, 10281_G|A, 10361_T|C, 10376_G|A, 10386_A|G, 10392_A|G, 10477_T|C, 10561_T|C
 Case 3 (A.1): OQ165285.1




Target: 995 samples       Number of changes: 469                                                                    


BC: A.1 + A.1.NmC1 + A.1  BC BR: 463-464, 466-467                   BC BR coord: 10391 - 10392, 10611 - 10612


Direction L1: >>          Initial region span: 1-463,464-466,467-469Gap history (edge excluded): 463-467 ->  


Alt. candidates: [], []                                                                                                    


Model 1BP/2BP comparison: 2BP vs 1BP: 4.70e-03                                                                             


Rec. model vs L1: 1.28e-02Rec. model vs L2: 0.00e+00                                                                


Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 463 49.059057 None None None * * *
|||||

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 466 3.420355 NaN NaN NaN * * *
A.1 995 464 -0.710160 -1.941794 9.883589 4.700906e-03 *
A.1.NmC2 83 464 -10.000000 -19.755055 45.510109 8.614407e-11
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 467 0.705991 None None None * * *



Target sequence

, 206_G|A, 212_C|T, 233_G|A, 254_A|G, 257_T|A, 266_T|C, 320_A|C, 419_A|T, 428_T|C, 431_T|C, 467_T|C, 475_C|T, 485_T|C, 515_G|A, 523_A|G, 534_G|A, 558_T|C, 564_A|G, 578_T|C, 617_C|A, 639_C|T,
653_G|A, 674_T|C, 689_G|A, 692_A|G, 734_A|G, 770_C|T, 803_A|G, 842_T|C, 878_C|T, 884_A|G, 899_C|T, 957_C|T, 977_C|T, 1007_C|T, 1034_T|C, 1070_C|T, 1091_A|G, 1094_G|A, 1100_C|T, 1103_C|T,
1110_C|T, 1115_T|C, 1124_A|G, 1127_C|T, 1160_T|C, 1175_A|G, 1232_A|G, 1250_C|T, 1277_C|T, 1298_T|C, 1328_T|C, 1355_C|T, 1379_T|C, 1433_C|T, 1444_C|T, 1520_G|A, 1607_C|T, 1616_C|G, 1634_C|T,
1644_T|C, 1655_C|T, 1682_C|T, 1701_C|T, 1769_A|C, 1781_C|T, 1793_T|C, 1854_C|T, 1865_T|C, 1898_G|A, 1907_A|G, 1940_A|G, 1946_C|T, 1973_C|T, 1991_T|C, 2021_C|T, 2066_C|T, 2069_A|G, 2090_C|T,
2093_T|A, 2103_C|T, 2114_T|C, 2129_C|T, 2150_C|T, 2156_G|T, 2198_T|C, 2228_T|C, 2279_T|C, 2285_C|T, 2381_T|A, 2394_A|G, 2437_T|C, 2469_T|C, 2474_C|T, 2501_C|T, 2525_G|A, 2540_A|G, 2606_C|T,
2633_A|G, 2648_T|G, 2654_C|T, 2681_G|A, 2687_C|T, 2723_CT|TC, 2792_A|G, 2798_A|G, 2804_C|T, 2816_C|T, 2831_C|T, 2840_T|C, 2858_C|T, 2864_A|G, 2876_A|C, 2879_T|C, 2891_C|T, 2921_A|G, 2925_G|A,
2930_T|C, 2963_T|C, 2996_C|T, 2999_G|A, 3002_T|C, 3008_A|G, 3014_T|C, 3038_T|C, 3041_T|A, 3052_T|C, 3059_G|A, 3068_T|C, 3071_A|G, 3104_G|A, 3110_T|C, 3134_C|T, 3137_T|C, 3140_A|G, 3180_T|C,
3186_G|A, 3203_G|A, 3218_T|A, 3221_C|T, 3248_T|C, 3254_T|C, 3275_C|T, 3279_A|G, 3290_A|G, 3296_C|T, 3314_T|C, 3329_C|T, 3332_G|A, 3338_T|C, 3368_A|G, 3377_A|G, 3380_T|C, 3434_G|A, 3450_C|T,
3464_T|A, 3506_A|G, 3515_A|G, 3518_C|T, 3522_T|C, 3534_G|A, 3666_C|T, 3705_C|T, 3723_T|C, 3731_C|T, 3806_A|C, 3818_A|C, 3836_T|C, 3854_A|G, 3881_T|C, 3885_T|C, 3895_C|T, 3906_T|C, 3973_T|C,
3989_T|C, 4034_G|A, 4049_G|A, 4076_C|T, 4085_T|C, 4106_A|G, 4112_C|T, 4128_T|C, 4146_C|T, 4172_C|T, 4238_C|T, 4268_C|T, 4272_T|C, 4277_T|C, 4292_G|A, 4322_C|T, 4325_G|A, 4328_C|T, 4331_T|C,
4343_C|T, 4424_C|T, 4436_T|C, 4454_G|A, 4493_C|T, 4589_C|T, 4592_A|G, 4595_C|T, 4610_A|G, 4682_C|T, 4688_A|G, 4697_T|C, 4733_T|C, 4751_T|C, 4790_A|G, 4829_C|T, 4856_T|C, 4859_A|G, 4877_C|T,
4886_G|A, 4904_C|T, 4961_T|C, 4982_T|C, 4988_G|A, 4994_G|T, 5000_T|C, 5027_A|G, 5060_T|C, 5090_G|A, 5144_G|A, 5153_G|A, 5189_A|G, 5192_CT|TC, 5267_T|C, 5270_T|G, 5277_T|C, 5279_A|G, 5342_T|C,
5357_C|T, 5375_A|G, 5387_C|T, 5390_C|T, 5420_T|C, 5429_G|A, 5432_A|C, 5435_C|T, 5450_T|C, 5456_G|T, 5459_T|C, 5516_T|A, 5567_G|A, 5582_T|C, 5600_C|T, 5612_T|C, 5621_C|A, 5723_T|C, 5732_A|G,
5747_G|A, 5811_C|A, 5828_T|C, 5834_G|A, 5846_T|C, 5867_T|C, 5879_T|G, 5903_A|G, 5937_T|C, 6027_C|A, 6056_C|T, 6092_C|T, 6098_C|T, 6101_T|C, 6152_C|T, 6155_A|G, 6299_C|T, 6363_C|T, 6443_G|A,
6446_G|A, 6473_T|C, 6524_A|G, 6527_C|T, 6584_T|C, 6608_G|A, 6618_C|T, 6629_T|C, 6641_G|T, 6671_T|C, 6674_C|T, 6684_A|C, 6725_T|C, 6737_C|T, 6746_C|T, 6797_T|C, 6803_C|T, 6842_A|G, 6872_C|T,
6890_A|G, 6908_T|A, 6944_G|A, 6954_A|G, 6983_A|G, 6992_A|G, 7014_C|T, 7037_C|T, 7046_T|C, 7049_CT|TC, 7059_T|C, 7064_T|C, 7085_A|G, 7088_G|A, 7136_T|C, 7151_T|C, 7175_C|T, 7178_A|G, 7187_T|C,
7208_A|G, 7233_C|T, 7239_C|T, 7257_T|C, 7292_G|T, 7295_G|A, 7307_T|G, 7313_T|C, 7430_G|A, 7451_AG|CA, 7460_C|T, 7464_A|G, 7466_A|T, 7470_TC|CT, 7475_G|C, 7550_C|T, 7553_G|A, 7568_T|C,
7625_A|T, 7628_C|T, 7633_T|C, 7653_T|C, 7670_G|A, 7679_A|G, 7694_A|G, 7713_T|C, 7739_C|T, 7769_G|A, 7784_G|A, 7805_T|C, 7808_T|A, 7817_G|A, 7844_T|C, 7853_G|T, 7869_C|A, 7871_G|A, 7964_A|G,
7982_A|G, 8007_GT|AC, 8027_G|A, 8069_T|C, 8078_T|G, 8082_C|T, 8093_G|T, 8159_C|A, 8198_A|G, 8213_A|G, 8237_T|C, 8252_G|A, 8353_C|T, 8393_G|A, 8408_T|C, 8450_T|C, 8459_G|A, 8467_T|C, 8477_T|C,
8490_A|C, 8511_A|G, 8516_A|G, 8534_C|T, 8555_C|T, 8570_T|C, 8591_A|G, 8597_T|C, 8606_C|T, 8624_C|T, 8630_A|C, 8660_A|G, 8720_T|C, 8771_A|G, 8789_T|G, 8794_G|A, 8811_T|C, 8813_G|A, 8819_A|G,
8828_C|T, 8849_C|T, 8852_T|C, 8873_C|T, 8882_T|C, 8895_T|C, 8897_A|G, 8918_A|G, 8924_G|A, 8969_T|C, 8997_C|T, 9011_C|T, 9017_T|C, 9050_G|A, 9053_A|G, 9092_C|T, 9098_T|C, 9128_C|T, 9176_C|T,
9215_C|T, 9224_C|T, 9233_G|A, 9239_T|C, 9244_T|C, 9256_G|A, 9272_C|T, 9275_T|C, 9299_C|T, 9305_C|T, 9326_A|G, 9353_T|C, 9365_A|G, 9427_A|G, 9434_A|G, 9449_T|C, 9452_T|C, 9455_G|A, 9470_G|A,
9488_C|T, 9503_C|T, 9509_T|C, 9518_A|G, 9527_A|G, 9539_T|C, 9582_C|T, 9585_C|A, 9591_T|C, 9599_A|G, 9607_A|G, 9668_C|T, 9677_G|A, 9713_C|T, 9722_T|C, 9728_A|G, 9749_A|G, 9774_GA|AG, 9806_C|T,
9821_CC|TT, 9824_T|C, 9851_T|C, 9857_C|T, 9884_G|A, 9896_T|A, 9950_G|A, 9965_C|T, 10004_T|C, 10052_T|C, 10094_A|G, 10148_A|G, 10163_T|C, 10208_G|A, 10223_C|T, 10238_G|A, 10244_C|T, 10247_C|T,
10266_A|G, 10331_C|T, 10361_T|C, 10374_C|T, 10376_G|A, 10388_C|T, 10392_A|G, 10477_T|C, 10561_T|C, 10612_T|C, 10654_A|G, 10666_T|C
 Case 3 (A.1): PQ849442.1




Target: 995 samples        Number of changes: 180                                               


BC: A.1 + A.1.NmC1         BC BR: 176-177                    BC BR coord: 10391 - 10392  


Direction L1: >>           Initial region span: 1-176,177-180Gap history (edge excluded):


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison:  -                                                                           


Rec. model vs L1: 6.96e-02 Rec. model vs L2: 0.00e+00                                           


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 176 3.733704 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 177 3.420355 None None None * * *



Target sequence

, 122_A|G, 254_A|G, 359_C|T, 423_G|A, 467_T|C, 475_C|T, 496_G|A, 523_A|G, 558_T|A, 653_G|A, 719_T|C, 803_A|G, 837_T|C, 1070_C|T, 1175_A|G, 1337_A|T, 1343_C|T, 1442_C|T, 1616_C|T, 1736_A|G,
1865_T|C, 1922_C|T, 2066_C|T, 2093_T|C, 2111_T|G, 2156_G|A, 2282_A|G, 2285_C|T, 2298_T|C, 2375_C|T, 2394_A|G, 2411_C|T, 2525_G|A, 2570_C|T, 2606_C|T, 2648_T|G, 2654_C|T, 2681_G|A, 2724_T|C,
2828_C|T, 2864_A|G, 2925_G|A, 3018_T|C, 3020_A|C, 3038_T|C, 3050_T|C, 3052_T|C, 3059_G|A, 3071_A|G, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3203_G|A, 3218_T|A, 3254_T|C, 3296_C|T, 3332_G|A,
3473_C|T, 3518_C|T, 3534_G|A, 3605_G|A, 3617_G|A, 3731_C|T, 3767_A|T, 3806_A|T, 3827_C|T, 3854_A|G, 3885_T|C, 3928_T|C, 3989_T|C, 4085_T|C, 4094_C|T, 4106_A|G, 4238_C|T, 4295_A|G, 4454_G|A,
4481_G|A, 4493_C|T, 4523_G|A, 4536_A|G, 4592_A|G, 4595_C|T, 4733_T|C, 4751_T|C, 4988_G|A, 5000_T|C, 5012_A|T, 5015_T|C, 5036_C|T, 5060_T|C, 5066_C|T, 5096_T|C, 5267_T|C, 5369_C|T, 5375_A|G,
5387_C|T, 5561_C|T, 5591_T|C, 5717_C|T, 5828_T|C, 5937_T|C, 6002_T|C, 6056_C|T, 6092_C|T, 6101_T|C, 6164_C|T, 6363_C|T, 6443_G|A, 6473_T|C, 6512_C|T, 6533_A|G, 6584_T|C, 6608_G|A, 6626_C|T,
6629_T|C, 6684_A|C, 6746_C|T, 6890_A|G, 6983_A|G, 6989_C|T, 7037_C|T, 7049_CT|TC, 7148_T|C, 7157_C|T, 7175_C|T, 7451_A|T, 7493_G|T, 7517_C|T, 7538_A|G, 7568_T|C, 7577_T|C, 7604_T|C, 7633_T|C,
7679_A|G, 7713_T|C, 7805_T|C, 7826_T|C, 7869_C|A, 7937_C|T, 8007_G|A, 8105_C|T, 8387_C|T, 8408_T|C, 8429_G|A, 8516_A|G, 8597_T|C, 8823_C|T, 8888_T|C, 9017_T|C, 9098_T|C, 9176_C|T, 9200_G|A,
9225_C|T, 9272_C|T, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9503_C|T, 9527_A|G, 9623_C|T, 9677_G|A, 9704_C|T, 9758_A|G, 9884_G|A, 9887_C|T, 9896_T|A, 9899_A|G, 10217_A|G, 10281_G|A,
10286_C|T, 10314_A|G, 10349_T|C, 10361_T|C, 10376_G|A, 10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): ON142674.1




Target: 995 samples        Number of changes: 116                                                 


BC: A.1.NmC1 + A.1         BC BR: 6-7                     BC BR coord: 754 - 755           


Direction L1: <<           Initial region span: 1-6,60-116Gap history (edge excluded): 6-60


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison:  -                                                                             


Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.69e+05                                             


Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 6 -8.607189 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 60 1.413718 NaN NaN NaN * * *
A.1.NmC1 181 114 0.478191 -543.503873 1385.007746 2.170770e-236



Target sequence

, 94_G|A, 254_A|G, 523_A|G, 558_T|C, 578_T|C, 653_G|A, 878_C|T, 1067_T|C, 1073_C|T, 1175_A|G, 1403_A|G, 1799_G|A, 1902_A|G, 2031_C|T, 2375_C|T, 2471_A|G, 2552_C|T, 2654_C|T, 2681_G|A,
2724_T|C, 2750_G|A, 2925_G|A, 3059_G|A, 3077_T|C, 3137_TC|CT, 3140_A|G, 3158_T|C, 3167_A|T, 3186_G|A, 3218_T|A, 3254_T|C, 3332_G|A, 3392_C|T, 3464_T|A, 3473_C|T, 3518_C|T, 3534_G|A, 3587_T|C,
3731_C|T, 4005_A|G, 4013_T|C, 4083_T|C, 4085_T|C, 4104_G|A, 4108_A|G, 4166_G|A, 4238_C|T, 4256_T|A, 4316_C|T, 4454_G|A, 4547_C|T, 4766_C|T, 4905_T|C, 5000_T|C, 5021_A|G, 5060_T|C, 5156_T|C,
5327_G|A, 5375_A|G, 5390_CT|TC, 5420_T|C, 5513_C|T, 5585_C|T, 5591_T|C, 5621_C|T, 5705_A|G, 5810_A|G, 5828_T|C, 5937_T|C, 6056_C|T, 6140_A|G, 6254_T|C, 6363_C|T, 6434_G|A, 6674_C|T, 6889_T|C,
6971_G|A, 6983_A|G, 6992_A|G, 7014_C|T, 7322_G|A, 7451_A|C, 7517_C|T, 7530_T|C, 7633_T|C, 7646_C|T, 7706_G|A, 7730_C|T, 7805_T|C, 8007_G|A, 8069_T|C, 8082_C|T, 8144_A|T, 8186_A|G, 8222_C|T,
8353_C|T, 8369_C|T, 8381_G|A, 8408_T|C, 8537_G|A, 8702_C|T, 8762_A|G, 8968_CT|TC, 9017_T|C, 9305_C|T, 9353_T|C, 9434_A|G, 9473_G|C, 9533_T|C, 9623_C|T, 9722_T|C, 9854_C|T, 10392_AT|GC,
10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): OR264642.1




Target: 995 samples          Number of changes: 114                                                                  


BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 6-7, 109-110                  BC BR coord: 754 - 755, 10288 - 10289       


Direction L1: <<             Initial region span: 1-6,7-34,110-114Gap history (edge excluded): 6-110 -> 34-110


Alt. candidates: [], []                                                                                                     


Model 1BP/2BP comparison:    2BP vs 1BP: 8.06e-225                                                                          


Rec. model vs L1: 0.00e+00   Rec. model vs L2: 1.05e+00                                                              


Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 6 0.074291 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 34 2.218083 NaN NaN NaN * * *
A.1.NmC1 181 7 0.000000 -516.051549 1328.103099 8.057843e-225
A.1.NmC2 83 7 -2.088999 -816.622709 1929.245418 0.000000e+00
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 110 3.172373 None None None * * *



Target sequence

, 254_A|G, 308_T|C, 523_A|G, 558_T|C, 578_T|C, 653_G|A, 758_G|A, 776_C|T, 786_C|T, 878_C|T, 909_T|C, 986_C|T, 1067_T|C, 1073_C|T, 1175_A|G, 1616_C|T, 1799_G|A, 2210_T|C, 2375_C|T, 2471_A|G,
2552_C|T, 2654_C|T, 2681_G|A, 2696_A|G, 2724_T|C, 2750_G|A, 2848_A|G, 2925_G|A, 3059_G|A, 3061_A|T, 3137_TC|CT, 3140_A|G, 3158_T|C, 3167_A|T, 3186_G|A, 3218_T|A, 3254_T|C, 3332_G|A, 3464_T|A,
3518_C|T, 3534_G|A, 3731_C|T, 4005_A|G, 4013_T|C, 4083_T|C, 4085_T|C, 4104_G|A, 4108_A|G, 4166_G|A, 4454_G|A, 4547_C|T, 4766_C|T, 4905_T|C, 5000_T|C, 5021_A|G, 5060_T|C, 5156_T|C, 5327_G|A,
5375_A|G, 5390_CT|TC, 5420_T|C, 5585_C|T, 5591_T|C, 5675_T|C, 5828_T|C, 5937_T|C, 6056_C|T, 6140_A|G, 6248_G|A, 6254_T|C, 6363_C|T, 6674_C|T, 6818_G|A, 6887_A|G, 6983_A|G, 6991_TA|CG,
7014_C|T, 7322_G|A, 7451_A|C, 7517_C|T, 7530_T|C, 7633_T|C, 7646_C|T, 7730_C|T, 7805_T|C, 8007_G|A, 8024_T|C, 8082_C|T, 8123_T|C, 8144_A|T, 8186_A|G, 8207_T|C, 8222_C|T, 8353_C|T, 8369_C|T,
8408_T|C, 8702_C|T, 8969_T|C, 9017_T|C, 9122_A|G, 9197_G|A, 9305_C|T, 9353_T|C, 9434_A|G, 9509_T|C, 9515_C|T, 9722_T|C, 9854_C|T, 10028_T|C, 10392_A|G, 10477_T|C, 10549_C|T, 10561_T|C,
10613_C|T
 Case 3 (A.1): OM666892.1




Target: 995 samples       Number of changes: 182                                                                     


BC: A.1 + A.1.NmC1 + A.1  BC BR: 51-52, 59-60                    BC BR coord: 3136 - 3137, 3458 - 3459        


Direction L1: >>          Initial region span: 1-51,52-58,127-182Gap history (edge excluded): 51-127 -> 58-127


Alt. candidates: [], []                                                                                                     


Model 1BP/2BP comparison: 2BP vs 1BP: 7.86e-20                                                                              


Rec. model vs L1: 1.71e-01Rec. model vs L2: 0.00e+00                                                                 


Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 51 2.021809 None None None * * *
|||||

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 58 3.342467 NaN NaN NaN * * *
A.1 995 81 -0.046106 -1.364218 18.728437 6.297610e-02 *
A.1.NmC2 83 55 -9.870109 -39.829585 95.659169 1.241762e-18
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 127 1.15759 None None None * * *



Target sequence

, 75, 138, 188_T|C, 254_A|G, 299_T|C, 423_G|A, 523_A|G, 558_T|C, 653_G|A, 656_A|G, 719_T|C, 773_T|C, 797_G|A, 803_A|G, 884_A|G, 947_C|T, 953_AC|GT, 968_G|A, 1067_T|C, 1175_A|G, 1319_G|A,
1559_A|G, 1568_C|T, 1616_C|T, 1916_A|G, 2019_G|A, 2066_C|T, 2309_C|T, 2375_C|T, 2385_A|G, 2394_A|T, 2411_C|T, 2448_T|C, 2504_G|A, 2525_G|A, 2606_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2739_G|A,
2774_C|T, 2873_G|A, 2879_T|C, 2925_G|A, 2949_C|A, 2969_C|T, 2984_T|C, 3038_T|C, 3041_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3228_T|C, 3254_T|C, 3332_G|A, 3338_T|C,
3518_C|T, 3534_G|A, 3566_T|C, 3596_G|A, 3615_C|T, 3671_A|G, 3718_C|T, 3731_C|T, 3836_T|C, 3857_C|T, 3881_T|C, 3908, 3989_T|C, 4085_T|C, 4106_A|G, 4133_A|T, 4167_C|T, 4220_G|A, 4322_C|T,
4337_A|G, 4403_A|C, 4409_A|G, 4454_G|A, 4499_C|T, 4523_G|A, 4925_G|A, 4934_G|A, 4961_T|C, 5000_T|C, 5030_C|T, 5042_T|C, 5060_T|C, 5096_T|C, 5256_A|G, 5279_A|G, 5297_C|T, 5375_A|G, 5387_C|T,
5421_C|T, 5459_T|C, 5483_A|G, 5555_C|T, 5591_T|C, 5642_A|G, 5717_C|T, 5753_A|G, 5798_C|T, 5828_T|C, 5937_T|C, 6029_G|A, 6056_C|T, 6143_T|C, 6176_G|A, 6383_C|A, 6422_T|C, 6545_C|T, 6557_C|T,
6608_G|A, 6645_C|T, 6684_A|C, 6807_T|C, 6827_T|A, 6839_G|A, 6953, 6980_G|A, 6983_A|G, 7050_T|C, 7172, 7316_T|C, 7343_C|T, 7451_A|C, 7502_G|A, 7517_C|T, 7568_T|C, 7598_G|A, 7633_T|C, 7637_A|G,
7784_G|A, 7805_T|C, 7808_T|C, 7880_G|A, 7887_T|C, 7964_A|G, 7973_A|G, 8007_G|A, 8018_A|G, 8063_C|T, 8069_T|C, 8213_A|G, 8237_T|C, 8303_C|T, 8408_T|C, 8474_C|T, 8504_T|C, 8588_T|C, 8591_A|G,
8606_C|T, 8631_A|G, 8780_T|C, 9011_C|T, 9017_T|C, 9239_T|C, 9305_C|T, 9329_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9506_A|T, 9515_C|T, 9616_A|T, 9704_C|T, 10004_T|C, 10163_T|C, 10206_T|C,
10322_C|T, 10361_T|C, 10376_G|A, 10383_C|T, 10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T, 10711
 Case 3 (A.1): OM666893.1




Target: 995 samples       Number of changes: 181                                                       


BC: A.1 + A.1             BC BR: 163-164                    BC BR coord: 9439 - 9440            


Direction L1: >>          Initial region span: 1-161,179-181Gap history (edge excluded): 161-179


Alt. candidates: [], []                                                                                       


Model 1BP/2BP comparison: 1BP vs 2BP: 8.64e-18                                                                


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                                   


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 161 2.08581 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 179 0.437871 None None None * * *



Target sequence

, 80, 138, 188_T|C, 254_A|G, 299_T|C, 423_G|A, 523_A|G, 558_T|C, 653_G|A, 656_A|G, 719_T|C, 773_T|C, 797_G|A, 803_A|G, 884_A|G, 947_C|T, 953_AC|GT, 968_G|A, 1067_T|C, 1175_A|G, 1319_G|A,
1559_A|G, 1568_C|T, 1616_C|T, 1916_A|G, 2019_G|A, 2066_C|T, 2309_C|T, 2375_C|T, 2385_A|G, 2394_A|T, 2411_C|T, 2448_T|C, 2504_G|A, 2525_G|A, 2606_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2739_G|A,
2774_C|T, 2873_G|A, 2879_T|C, 2925_G|A, 2949_C|A, 2969_C|T, 2984_T|C, 3038_T|C, 3041_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3228_T|C, 3254_T|C, 3332_G|A, 3338_T|C,
3518_C|T, 3534_G|A, 3566_T|C, 3596_G|A, 3615_C|T, 3671_A|G, 3718_C|T, 3731_C|T, 3836_T|C, 3857_C|T, 3881_T|C, 3908, 3989_T|C, 4085_T|C, 4106_A|G, 4133_A|T, 4167_C|T, 4220_G|A, 4322_C|T,
4337_A|G, 4403_A|C, 4409_A|G, 4454_G|A, 4499_C|T, 4523_G|A, 4925_G|A, 4934_G|A, 4961_T|C, 5000_T|C, 5030_C|T, 5042_T|C, 5060_T|C, 5096_T|C, 5256_A|G, 5279_A|G, 5297_C|T, 5375_A|G, 5387_C|T,
5421_C|T, 5459_T|C, 5483_A|G, 5555_C|T, 5591_T|C, 5642_A|G, 5717_C|T, 5753_A|G, 5798_C|T, 5828_T|C, 5937_T|C, 6029_G|A, 6056_C|T, 6143_T|C, 6176_G|A, 6383_C|A, 6422_T|C, 6545_C|T, 6557_C|T,
6608_G|A, 6645_C|T, 6684_A|C, 6807_T|C, 6827_T|A, 6839_G|A, 6953, 6980_G|A, 6983_A|G, 7050_T|C, 7172, 7316_T|C, 7343_C|T, 7451_A|C, 7502_G|A, 7517_C|T, 7568_T|C, 7598_G|A, 7633_T|C, 7637_A|G,
7784_G|A, 7805_T|C, 7808_T|C, 7880_G|A, 7887_T|C, 7964_A|G, 7973_A|G, 8007_G|A, 8018_A|G, 8063_C|T, 8069_T|C, 8213_A|G, 8237_T|C, 8303_C|T, 8408_T|C, 8474_C|T, 8504_T|C, 8588_T|C, 8591_A|G,
8606_C|T, 8631_A|G, 8780_T|C, 9239_T|C, 9305_C|T, 9329_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9506_A|T, 9515_C|T, 9616_A|T, 9704_C|T, 10004_T|C, 10163_T|C, 10206_T|C, 10322_C|T, 10361_T|C,
10376_G|A, 10383_C|T, 10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T, 10711, 10749_T|G
 Case 3 (A.1): OM666891.1




Target: 995 samples       Number of changes: 177                                                                     


BC: A.1 + A.1.NmC1 + A.1  BC BR: 53-54, 70-71                    BC BR coord: 3136 - 3137, 3898 - 3899        


Direction L1: >>          Initial region span: 1-53,54-62,123-177Gap history (edge excluded): 53-123 -> 62-123


Alt. candidates: [], []                                                                                                     


Model 1BP/2BP comparison: 2BP vs 1BP: 3.35e-01                                                                              


Rec. model vs L1: 5.90e+27Rec. model vs L2: 0.00e+00                                                                 


Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 53 1.738698 None None None * * *
|||||

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 62 5.071491 NaN NaN NaN * * *
A.1 995 80 -0.617934 -1.060408 38.120816 2.667265e+17 *
A.1.NmC2 83 57 -9.870109 -101.010280 238.020560 1.043116e-26
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 123 0.964819 None None None * * *



Target sequence

, 80, 138, 188_T|C, 254_A|G, 299_T|C, 423_G|A, 523_A|G, 558_T|C, 653_G|A, 656_A|G, 719_T|C, 773_T|C, 797_G|A, 803_A|G, 884_A|G, 947_C|T, 953_AC|GT, 968_G|A, 1067_T|C, 1175_A|G, 1343_C|T,
1559_A|G, 1568_C|T, 1616_C|T, 2019_G|A, 2066_C|T, 2093_T|C, 2096_G|A, 2309_C|T, 2375_C|T, 2385_A|G, 2394_A|T, 2411_C|T, 2448_T|C, 2504_G|A, 2522_G|A, 2525_G|A, 2606_C|T, 2627_C|T, 2654_C|T,
2681_G|A, 2724_T|C, 2739_G|A, 2774_C|T, 2873_G|A, 2879_T|C, 2925_G|A, 2949_C|A, 2969_C|T, 2984_T|C, 3038_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3228_T|C, 3254_T|C,
3332_G|A, 3518_C|T, 3534_G|A, 3566_T|C, 3596_G|A, 3671_A|G, 3718_C|T, 3731_C|T, 3836_T|C, 3857_C|T, 3881_T|C, 3989_T|C, 4085_T|C, 4106_A|G, 4133_A|T, 4167_C|T, 4220_G|A, 4322_C|T, 4337_A|G,
4403_A|C, 4409_A|G, 4454_G|A, 4499_C|T, 4523_G|A, 4925_G|A, 4934_G|A, 4961_T|C, 5000_T|C, 5030_C|T, 5042_T|C, 5060_T|C, 5096_T|C, 5256_A|G, 5279_A|G, 5297_C|T, 5375_A|G, 5387_C|T, 5421_C|T,
5459_T|C, 5483_A|G, 5555_C|T, 5591_T|C, 5642_A|G, 5717_C|T, 5753_A|G, 5798_C|T, 5828_T|C, 5937_T|C, 6029_G|A, 6056_C|T, 6062_C|T, 6143_T|C, 6176_G|A, 6422_T|C, 6545_C|T, 6557_C|T, 6645_C|T,
6684_A|C, 6807_T|C, 6827_T|A, 6839_G|A, 6983_A|G, 7050_T|C, 7172, 7238_C|T, 7316_T|C, 7343_C|T, 7451_A|C, 7502_G|A, 7517_C|T, 7568_T|C, 7598_G|A, 7633_T|C, 7637_A|G, 7784_G|A, 7805_T|C,
7808_T|C, 7880_G|A, 7887_T|C, 7964_A|G, 7973_A|G, 8007_G|A, 8018_A|G, 8063_C|T, 8069_T|C, 8213_A|G, 8303_C|T, 8408_T|C, 8474_C|T, 8504_T|C, 8588_T|C, 8591_A|G, 8606_C|T, 8631_A|G, 8780_T|C,
9011_C|T, 9017_T|C, 9239_T|C, 9305_C|T, 9329_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9506_A|T, 9515_C|T, 9616_A|T, 9704_C|T, 10004_T|C, 10163_T|C, 10322_C|T, 10361_T|C, 10376_G|A, 10383_C|T,
10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T, 10711
 Case 3 (A.1): OQ734448.1




Target: 995 samples        Number of changes: 117                                                 


BC: A.1.NmC1 + A.1         BC BR: 6-7                     BC BR coord: 754 - 755           


Direction L1: >>           Initial region span: 1-6,65-117Gap history (edge excluded): 6-65


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison:  -                                                                             


Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.36e-01                                             


Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 6 2.183765 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 65 1.198407 None None None * * *



Target sequence

, 254_A|G, 523_A|G, 558_T|C, 578_T|C, 653_G|A, 746_T|C, 878_C|T, 890_A|C, 908_T|G, 932_A|G, 1067_T|C, 1073_C|T, 1115_T|C, 1175_A|G, 1433_C|T, 1616_C|T, 1730_A|G, 1799_G|A, 2210_T|C, 2375_C|T,
2426_T|C, 2471_A|G, 2552_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2750_G|A, 2925_G|A, 3059_G|A, 3137_TC|CT, 3140_A|G, 3158_T|C, 3167_A|T, 3171_T|A, 3186_G|A, 3218_T|A, 3230_A|T, 3254_T|C, 3332_G|A,
3387_T|A, 3464_T|A, 3518_C|T, 3534_G|A, 3731_C|T, 3767_A|G, 3954_T|C, 4005_A|G, 4013_T|A, 4085_T|C, 4104_G|A, 4108_A|G, 4166_G|A, 4433_C|T, 4454_G|A, 4514_C|T, 4547_C|T, 4766_C|T, 4905_T|C,
5000_T|C, 5021_A|G, 5060_T|C, 5156_T|C, 5327_G|A, 5375_A|G, 5390_CT|TC, 5420_T|C, 5552_C|T, 5585_C|T, 5591_T|C, 5759_G|A, 5828_T|C, 5937_T|C, 6056_C|T, 6101_T|C, 6123_A|G, 6140_A|G, 6254_T|C,
6363_C|T, 6500_A|G, 6626_C|T, 6636_T|C, 6674_C|T, 6983_A|G, 6992_A|G, 7014_C|T, 7322_G|A, 7451_A|C, 7517_C|T, 7530_T|C, 7633_T|C, 7646_C|T, 7730_C|T, 7805_T|C, 7832_G|C, 7877_C|T, 7949_C|T,
8007_G|A, 8082_C|T, 8144_A|T, 8186_A|G, 8222_C|T, 8353_C|T, 8369_C|T, 8408_T|C, 8702_C|T, 8895_T|C, 8969_T|C, 9017_T|C, 9179_A|G, 9305_C|T, 9353_T|C, 9434_A|G, 9728_A|G, 9854_C|T, 10001_C|T,
10037_T|C, 10052_T|C
 Case 3 (A.1): OR264643.1




Target: 995 samples          Number of changes: 130                                                                  


BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 8-9, 126-127                    BC BR coord: 754 - 755, 10391 - 10392     


Direction L1: >>             Initial region span: 1-4,68-126,127-130Gap history (edge excluded): 4-127 -> 4-68


Alt. candidates: [], []                                                                                                     


Model 1BP/2BP comparison:    2BP vs 1BP: 3.03e-272                                                                          


Rec. model vs L1: 0.00e+00   Rec. model vs L2: 5.76e+09                                                              


Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 4 2.664233 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 68 1.611904 NaN NaN NaN * * *
A.1.NmC2 83 127 0.000000 -984.519491 2295.038981 0.000000e+00
A.1.NmC1 181 127 -1.901631 -626.531442 1579.062883 3.028736e-272
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 127 1.925944 None None None * * *



Target sequence

, 254_A|G, 449_C|T, 523_A|G, 558_T|C, 560_G|A, 578_T|C, 614_C|A, 653_G|A, 878_C|T, 881_G|A, 932_A|G, 1067_T|C, 1073_C|T, 1175_A|G, 1241_T|A, 1340_C|T, 1616_C|T, 1799_G|A, 1815_G|A, 2210_T|C,
2375_C|T, 2471_A|G, 2552_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2750_G|A, 2840_T|C, 2858_C|T, 2925_G|A, 3059_G|A, 3137_T|C, 3140_A|G, 3158_T|C, 3167_A|T, 3182_G|A, 3186_G|A, 3218_T|A, 3233_T|C,
3254_T|C, 3332_G|A, 3464_T|A, 3518_C|T, 3534_G|A, 3705_C|T, 3731_C|T, 3899_C|T, 3935_T|C, 4005_A|G, 4013_T|A, 4061_A|G, 4085_T|C, 4104_G|A, 4108_A|G, 4166_G|A, 4445_C|T, 4454_G|A, 4517_A|G,
4547_C|T, 4766_C|T, 4905_T|C, 5000_T|C, 5021_A|G, 5060_T|C, 5156_T|C, 5327_G|A, 5375_A|G, 5390_CT|TC, 5420_T|C, 5525_G|A, 5552_C|T, 5585_C|T, 5591_T|C, 5621_C|T, 5792_A|G, 5828_T|C, 5937_T|C,
6056_C|T, 6140_A|G, 6254_T|C, 6363_C|T, 6674_C|T, 6953_A|G, 6983_A|G, 6988_C|A, 6992_A|G, 7014_C|T, 7025_C|T, 7322_G|A, 7361_G|A, 7451_A|C, 7457_C|T, 7467_C|T, 7517_C|T, 7530_T|C, 7633_T|C,
7646_C|T, 7713_T|C, 7730_C|T, 7805_T|C, 7814_A|G, 7888_A|C, 8006_CG|TA, 8082_C|T, 8144_A|T, 8186_A|G, 8190_A|G, 8222_C|T, 8312_T|C, 8353_C|T, 8369_C|T, 8408_T|C, 8467_T|C, 8702_C|T, 8811_T|C,
8969_T|C, 9017_T|C, 9305_C|T, 9346_A|G, 9353_T|C, 9389_C|T, 9434_A|G, 9728_A|G, 9761_C|A, 9854_C|T, 10142_C|T, 10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): OR264644.1




Target: 995 samples        Number of changes: 138                                                 


BC: A.1.NmC1 + A.1         BC BR: 7-8                     BC BR coord: 754 - 755           


Direction L1: <<           Initial region span: 1-6,86-138Gap history (edge excluded): 6-86


Alt. candidates: [], []                                                                                  


Model 1BP/2BP comparison:  -                                                                             


Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.54e+06                                             


Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 6 0.074291 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 86 2.510313 NaN NaN NaN * * *
A.1.NmC1 181 136 0.478191 -692.52304 1721.04608 2.005108e-302



Target sequence

, 254_A|G, 308_T|C, 523_A|G, 558_T|C, 578_T|C, 653_G|A, 727_A|G, 758_G|A, 786_C|T, 878_C|T, 909_T|C, 986_C|T, 1067_T|C, 1073_C|T, 1175_A|G, 1616_C|T, 1799_G|A, 2129_C|T, 2210_T|C, 2375_C|T,
2394_A|G, 2471_A|G, 2552_C|T, 2648_T|C, 2654_C|T, 2681_G|A, 2696_A|G, 2711_G|A, 2724_T|C, 2750_G|A, 2848_A|G, 2903_C|T, 2925_G|A, 3059_G|A, 3137_TC|CT, 3140_A|G, 3158_T|C, 3167_A|T, 3186_G|A,
3218_T|A, 3254_T|C, 3332_G|A, 3450_C|T, 3464_T|A, 3518_C|T, 3534_G|A, 3658_T|C, 3713_G|A, 3731_C|T, 4005_A|G, 4013_T|C, 4015_C|T, 4083_T|C, 4085_T|C, 4104_G|A, 4108_A|G, 4130_A|G, 4166_G|A,
4454_G|A, 4547_C|T, 4697_T|C, 4766_C|T, 4905_T|C, 5000_T|C, 5021_A|G, 5156_T|C, 5327_G|A, 5375_A|G, 5390_CT|TC, 5414_T|C, 5420_T|C, 5454_C|T, 5585_C|T, 5591_T|C, 5675_T|C, 5690_A|T, 5828_T|C,
5894_G|A, 5937_T|C, 5975_C|T, 6056_C|T, 6140_A|G, 6248_G|A, 6254_T|C, 6363_C|T, 6659_G|A, 6674_C|T, 6818_G|A, 6887_A|G, 6983_A|G, 6991_TA|CG, 7014_C|T, 7322_G|A, 7451_A|C, 7506_C|T, 7517_C|T,
7530_T|C, 7532_G|A, 7607_C|T, 7629_T|C, 7633_T|C, 7646_C|T, 7730_C|T, 7805_T|C, 7865_G|A, 8007_G|A, 8024_T|C, 8082_C|T, 8097_C|T, 8123_T|C, 8144_A|T, 8186_A|G, 8207_T|C, 8222_C|T, 8353_C|T,
8369_C|T, 8408_T|C, 8504_T|C, 8534_C|T, 8547_T|C, 8702_C|T, 8735_C|T, 8969_T|C, 9017_T|C, 9197_G|A, 9305_C|T, 9348_G|A, 9353_T|C, 9434_A|G, 9515_C|T, 9722_T|C, 9854_C|T, 10028_T|C, 10392_A|G,
10470_C|T, 10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): OR264645.1




Target: 995 samples          Number of changes: 130                                                                    


BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 4-5, 126-127                   BC BR coord: 559 - 560, 10288 - 10289        


Direction L1: >>             Initial region span: 1-4,5-121,127-130Gap history (edge excluded): 4-127 -> 121-127


Alt. candidates: [], []                                                                                                       


Model 1BP/2BP comparison:    2BP vs 1BP: 2.38e-279                                                                            


Rec. model vs L1: 0.00e+00   Rec. model vs L2: 4.45e-01                                                                


Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 4 2.664233 NaN NaN NaN * * *
A.1 995 121 0.218010 -4.105711 28.211422 0.001119 *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 121 2.584467 NaN NaN NaN * * *
A.1.NmC2 83 5 -10.000000 -1003.051318 2340.102636 0.000000e+00
A.1.NmC1 181 5 -10.000000 -640.493819 1614.987637 2.377955e-279
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 127 1.925944 None None None * * *



Target sequence

, 254_A|G, 449_C|T, 523_A|G, 558_T|C, 560_G|A, 578_T|C, 639_C|T, 653_G|A, 878_C|T, 881_G|A, 932_A|G, 1067_T|C, 1073_C|T, 1175_A|G, 1265_A|G, 1340_C|T, 1478_T|C, 1616_C|T, 1799_G|A, 1815_G|A,
1922_C|T, 2030_T|C, 2210_T|C, 2375_C|T, 2471_A|G, 2552_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2750_G|A, 2840_T|C, 2925_G|A, 3050_T|C, 3059_G|A, 3137_TC|CT, 3140_A|G, 3158_T|C, 3167_A|T, 3186_G|A,
3218_T|A, 3233_T|C, 3254_T|C, 3332_G|A, 3464_T|A, 3518_C|T, 3534_G|A, 3650_C|T, 3731_C|T, 3935_T|C, 4005_A|G, 4013_T|A, 4061_A|G, 4085_T|C, 4104_G|A, 4108_A|G, 4166_G|A, 4454_G|A, 4547_C|T,
4766_C|T, 4785_C|T, 4905_T|C, 5000_T|C, 5021_A|G, 5060_T|C, 5081_C|A, 5156_T|C, 5189_A|G, 5327_G|A, 5375_A|G, 5390_CT|TC, 5417_A|G, 5420_T|C, 5525_G|A, 5552_C|T, 5585_C|T, 5591_T|C, 5627_G|T,
5828_T|C, 5937_T|C, 6056_C|T, 6137_T|C, 6140_A|G, 6254_T|C, 6363_C|T, 6674_C|T, 6740_A|T, 6953_A|G, 6983_A|G, 6988_C|A, 6992_A|G, 7014_C|T, 7322_G|A, 7361_G|A, 7451_A|C, 7467_C|T, 7517_C|T,
7530_T|C, 7633_T|C, 7646_C|T, 7713_T|C, 7730_C|T, 7805_T|C, 7888_A|C, 8007_G|A, 8082_C|T, 8144_A|T, 8186_A|G, 8222_C|T, 8312_T|C, 8353_C|T, 8369_C|T, 8408_T|C, 8467_T|C, 8496_A|G, 8702_C|T,
8969_T|C, 9017_T|C, 9305_C|T, 9346_A|G, 9353_T|C, 9389_C|T, 9434_A|G, 9572_C|T, 9728_A|G, 9761_C|A, 9854_C|T, 10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): OR264646.1




Target: 995 samples          Number of changes: 136                                                                  


BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 4-5, 132-133                  BC BR coord: 559 - 560, 10288 - 10289       


Direction L1: >>             Initial region span: 1-4,5-42,133-136Gap history (edge excluded): 4-133 -> 42-133


Alt. candidates: [], []                                                                                                     


Model 1BP/2BP comparison:    2BP vs 1BP: 3.27e-294                                                                          


Rec. model vs L1: 0.00e+00   Rec. model vs L2: 4.45e-01                                                              


Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 4 2.664233 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 42 1.866708 NaN NaN NaN * * *
A.1.NmC2 83 5 -10.000000 -1072.311084 2488.622168 0.000000e+00
A.1.NmC1 181 5 -10.000000 -677.526440 1699.052880 3.270744e-294
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 133 1.925944 None None None * * *



Target sequence

, 254_A|G, 449_C|T, 523_A|G, 558_T|C, 560_G|A, 578_T|C, 614_C|A, 653_G|A, 878_C|T, 881_G|A, 932_A|G, 1067_T|C, 1073_C|T, 1175_A|G, 1241_T|A, 1340_C|T, 1616_C|T, 1799_G|A, 1815_G|A, 2210_T|C,
2375_C|T, 2388_T|C, 2391_C|T, 2471_A|G, 2552_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2750_G|A, 2840_T|C, 2858_C|T, 2925_G|A, 3059_G|A, 3137_T|C, 3140_A|G, 3158_T|C, 3167_A|T, 3182_G|A, 3186_G|A,
3218_T|A, 3230_A|G, 3233_T|C, 3254_T|C, 3332_G|A, 3464_T|A, 3518_C|T, 3534_G|A, 3705_C|T, 3731_C|T, 3899_C|T, 3935_T|C, 4005_A|G, 4013_T|A, 4061_A|G, 4085_T|C, 4104_G|A, 4108_A|G, 4166_G|A,
4445_C|T, 4454_G|A, 4547_C|T, 4766_C|T, 4905_T|C, 5000_T|C, 5021_A|G, 5060_T|C, 5156_T|C, 5327_G|A, 5375_A|G, 5390_CT|TC, 5420_T|C, 5525_G|A, 5552_C|T, 5585_C|T, 5591_T|C, 5621_C|T, 5792_A|G,
5828_T|C, 5937_T|C, 6056_C|T, 6140_A|G, 6254_T|C, 6363_C|T, 6674_C|T, 6890_A|G, 6953_A|G, 6983_A|G, 6988_C|A, 6992_A|G, 7014_C|T, 7025_C|T, 7322_G|A, 7361_G|A, 7451_A|C, 7457_C|T, 7467_C|T,
7517_C|T, 7530_T|C, 7633_T|C, 7646_C|T, 7713_T|C, 7730_C|T, 7805_T|C, 7814_A|G, 7888_A|C, 8006_CG|TA, 8082_C|T, 8144_A|T, 8186_A|G, 8190_A|G, 8222_C|T, 8312_T|C, 8353_C|T, 8369_C|T, 8408_T|C,
8467_T|C, 8702_C|T, 8811_T|C, 8828_C|T, 8852_T|C, 8969_T|C, 9017_T|C, 9305_C|T, 9346_A|G, 9353_T|C, 9389_C|T, 9434_A|G, 9728_A|G, 9745_C|T, 9761_C|A, 9854_C|T, 10142_C|T, 10392_A|G,
10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): OR264647.1




Target: 995 samples        Number of changes: 133                                                     


BC: A.1 + A.1.NmC1         BC BR: 129-130                   BC BR coord: 10288 - 10289         


Direction L1: <<           Initial region span: 1-40,130-133Gap history (edge excluded): 40-130


Alt. candidates: [], []                                                                                      


Model 1BP/2BP comparison:  -                                                                                 


Rec. model vs L1: 9.92e+00 Rec. model vs L2: 0.00e+00                                                 


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 40 0.689759 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 130 1.925944 NaN NaN NaN * * *
A.1 995 71 0.803982 -1.739254 13.478508 0.171187 *



Target sequence

, 254_A|G, 459_A|G, 523_A|G, 558_T|C, 560_G|A, 578_T|C, 614_C|A, 647_G|A, 653_G|A, 878_C|T, 881_G|A, 932_A|G, 1067_T|C, 1073_C|T, 1175_A|G, 1241_T|A, 1340_C|T, 1616_C|T, 1799_G|A, 1815_G|A,
2210_T|C, 2375_C|T, 2471_A|G, 2552_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2750_G|A, 2840_T|C, 2855_C|T, 2858_C|T, 2925_G|A, 3059_G|A, 3137_TC|CT, 3140_A|G, 3158_T|C, 3167_A|T, 3186_G|A, 3218_T|A,
3233_T|C, 3254_T|C, 3332_G|A, 3464_T|A, 3518_C|T, 3534_G|A, 3632_C|T, 3731_C|T, 3899_C|T, 3926_T|C, 3935_T|C, 3986_T|C, 4005_A|G, 4013_T|A, 4030_C|T, 4061_A|G, 4085_T|C, 4104_G|A, 4108_A|G,
4166_G|A, 4445_C|T, 4454_G|A, 4547_C|T, 4766_C|T, 4905_T|C, 5000_T|C, 5021_A|G, 5060_T|C, 5156_T|C, 5327_G|A, 5375_A|G, 5390_CT|TC, 5417_A|C, 5420_T|C, 5525_G|A, 5552_C|T, 5585_C|T, 5591_T|C,
5792_A|G, 5828_T|C, 5937_T|C, 6056_C|T, 6140_A|G, 6254_T|C, 6363_C|T, 6674_C|T, 6953_A|G, 6983_A|G, 6988_C|A, 6992_A|G, 7014_C|T, 7112_C|T, 7322_G|A, 7361_G|A, 7451_A|C, 7457_C|T, 7467_C|T,
7517_C|T, 7530_T|C, 7633_T|C, 7646_C|T, 7713_T|C, 7730_C|T, 7805_T|C, 7814_A|G, 7888_A|C, 8007_G|A, 8082_C|T, 8144_A|T, 8186_A|G, 8222_C|T, 8283_C|T, 8312_T|C, 8348_C|T, 8353_C|T, 8369_C|T,
8408_T|C, 8467_T|C, 8702_C|T, 8969_T|C, 9017_T|C, 9305_C|T, 9346_A|G, 9353_T|C, 9389_C|T, 9434_A|G, 9676_A|G, 9728_A|G, 9761_C|A, 9854_C|T, 10392_A|G, 10477_T|C, 10561_T|C, 10613_C|T
 Case 3 (A.1): PQ008648.1




Target: 995 samples       Number of changes: 204                                                   


BC: A.1 + A.1             BC BR: 38-39                    BC BR coord: 2533 - 2534          


Direction L1: <<          Initial region span: 1-37,66-204Gap history (edge excluded): 37-66


Alt. candidates: [], []                                                                                   


Model 1BP/2BP comparison: 1BP vs 2BP: 1.06e-02                                                            


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                               


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 37 1.500082 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 66 5.547291 None None None * * *



Target sequence

, 188_T|C, 254_A|G, 299_T|C, 423_G|A, 482_C|T, 510_T|C, 523_A|G, 558_T|C, 584_G|A, 653_G|A, 719_T|C, 773_T|C, 803_A|G, 837_T|C, 872_T|C, 884_A|G, 914_A|G, 953_AC|GT, 1019_T|C, 1175_A|G,
1217_C|T, 1328_T|C, 1513_C|T, 1559_A|G, 1616_C|T, 1691_C|T, 1787_T|C, 1815_G|A, 1841_C|T, 1850_T|C, 1946_C|T, 2066_C|T, 2111_T|C, 2375_C|T, 2411_C|T, 2448_T|C, 2504_G|A, 2525_G|A, 2606_C|T,
2654_C|T, 2681_G|A, 2724_T|C, 2739_G|A, 2774_C|T, 2799_T|C, 2879_T|C, 2925_G|A, 2949_C|A, 2969_C|T, 3038_T|C, 3041_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3228_T|C,
3254_T|C, 3332_G|A, 3350_G|A, 3425_C|T, 3482_T|C, 3518_C|T, 3534_G|A, 3551_A|G, 3596_G|A, 3671_A|G, 3731_C|T, 3800_C|T, 3812_G|A, 3836_T|C, 3857_C|T, 3881_T|C, 3950_C|T, 3989_T|C, 4013_T|C,
4106_A|G, 4111_G|C, 4133_A|T, 4199_G|T, 4220_G|A, 4225_G|C, 4292_G|T, 4325_G|A, 4337_A|G, 4403_A|C, 4409_A|G, 4454_G|A, 4481_G|A, 4499_C|T, 4523_G|A, 4925_G|A, 4934_G|A, 5000_T|C, 5030_C|T,
5060_T|C, 5096_T|C, 5279_A|G, 5369_C|T, 5375_A|G, 5384_C|T, 5387_C|T, 5411_C|T, 5421_C|T, 5423_A|G, 5459_T|C, 5555_C|T, 5591_T|C, 5717_C|T, 5801_G|A, 5828_T|C, 5858_C|T, 5864_C|T, 6056_C|T,
6068_A|G, 6143_T|C, 6185_T|C, 6404_C|T, 6419_T|C, 6428_C|T, 6506_A|C, 6539_T|C, 6545_C|T, 6551_T|C, 6608_G|A, 6684_A|C, 6686_G|A, 6807_T|C, 6810_C|T, 6827_T|A, 6839_G|A, 6869_A|G, 6923_C|T,
6926_A|T, 6962_A|G, 6983_A|G, 7040_C|T, 7046_T|C, 7050_T|C, 7157_C|A, 7220_A|G, 7316_T|C, 7451_A|C, 7499_T|C, 7517_C|T, 7538_A|G, 7586_T|C, 7598_G|A, 7633_T|C, 7637_A|G, 7739_C|T, 7805_T|C,
7808_T|C, 7880_G|A, 7887_T|C, 7964_A|G, 8007_G|A, 8058_G|A, 8063_C|T, 8069_T|C, 8303_C|G, 8348_C|T, 8398_T|G, 8408_T|C, 8414_G|A, 8438_G|A, 8465_G|A, 8474_C|T, 8511_A|G, 8591_A|G, 8631_A|G,
8780_T|C, 8804_T|C, 9001_G|A, 9011_C|T, 9017_T|C, 9233_G|A, 9239_T|C, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9467_AA|CT, 9481_A|T, 9515_C|T, 9532_T|G, 9568_AA|GG, 9656_T|C, 9819_C|A,
9992_A|G, 10052_T|C, 10163_T|C, 10322_C|T, 10376_G|A, 10392_A|G, 10418_C|A, 10477_T|C, 10502_C|T, 10541_C|T, 10549_C|G, 10561_T|C, 10661_.|C, 10670_T|A
 Case 3 (A.1): PQ461653.1




Target: 995 samples       Number of changes: 186                                                     


BC: A.1 + A.1             BC BR: 69-70                     BC BR coord: 3458 - 3459           


Direction L1: <<          Initial region span: 1-61,114-186Gap history (edge excluded): 61-114


Alt. candidates: [], []                                                                                     


Model 1BP/2BP comparison: 1BP vs 2BP: 1.06e-06                                                              


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                                 


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 61 1.489549 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 114 1.717957 None None None * * *



Target sequence

, 150_A|C, 188_T|C, 254_A|G, 299_T|C, 398_T|C, 423_G|A, 523_A|G, 558_T|C, 653_G|A, 689_G|A, 719_T|C, 773_T|C, 779_T|C, 803_A|G, 848_C|T, 884_A|G, 953_A|G, 1175_A|G, 1559_A|G, 1607_C|T,
1616_C|T, 1775_C|T, 1787_T|C, 1815_G|A, 1826_G|A, 1871_T|C, 1976_A|G, 2036_C|T, 2066_C|T, 2129_C|T, 2219_T|C, 2233_A|G, 2312_C|A, 2375_C|T, 2411_C|T, 2435_T|C, 2448_T|C, 2471_A|G, 2486_T|C,
2504_G|A, 2522_G|A, 2525_G|A, 2537_T|C, 2606_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2739_G|A, 2774_C|T, 2879_T|C, 2925_G|A, 2948_TC|CA, 2969_C|T, 2972_G|A, 3038_T|C, 3041_T|C, 3059_G|A, 3089_C|T,
3110_T|C, 3123_C|T, 3128_G|A, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3221_C|T, 3228_T|C, 3254_T|C, 3332_G|A, 3518_C|T, 3524_A|G, 3534_G|A, 3596_G|A, 3671_A|G, 3674_T|C, 3731_C|T, 3780_C|T,
3836_T|C, 3857_C|T, 3881_T|C, 3989_T|C, 4085_T|C, 4106_A|G, 4133_A|T, 4167_C|T, 4220_G|A, 4238_C|T, 4328_C|T, 4337_A|G, 4367_T|C, 4403_A|C, 4409_A|G, 4454_G|A, 4499_C|T, 4523_G|A, 4733_T|C,
4757_T|A, 4901_G|A, 4925_G|A, 4934_G|A, 4979_C|G, 5000_T|C, 5030_C|T, 5043_G|T, 5060_T|C, 5096_T|C, 5210_G|A, 5240_C|T, 5270_T|A, 5279_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5421_C|T, 5459_T|C,
5462_T|A, 5591_T|C, 5621_C|T, 5717_C|T, 5937_T|C, 6056_C|T, 6137_T|C, 6143_T|C, 6239_T|C, 6269_C|T, 6425_G|A, 6545_C|T, 6674_C|T, 6684_A|C, 6807_T|C, 6827_T|A, 6839_G|A, 6884_A|G, 6902_C|T,
6953, 6960_C|T, 6983_A|G, 7046_T|C, 7050_T|C, 7133_A|G, 7197_C|T, 7316_T|C, 7451_A|C, 7460_C|T, 7517_C|T, 7598_G|A, 7604_T|C, 7633_T|C, 7637_A|G, 7643_A|G, 7805_T|C, 7808_T|C, 7869_C|A,
7880_G|A, 7887_T|C, 7937_C|T, 7964_A|G, 8007_G|A, 8018_A|G, 8063_C|T, 8246_A|G, 8303_C|T, 8318_T|C, 8408_T|C, 8474_C|T, 8591_A|G, 8606_C|T, 8631_A|G, 8780_T|C, 8951_C|T, 9011_C|T, 9017_T|C,
9197_G|A, 9239_T|C, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9515_C|T, 9656_T|C, 10010_T|C, 10262_T|C, 10322_C|T, 10376_G|A, 10392_A|G, 10477_T|C
 Case 3 (A.1): PV426612.1




Target: 995 samples       Number of changes: 185                                                   


BC: A.1 + A.1             BC BR: 38-39                    BC BR coord: 2533 - 2534          


Direction L1: <<          Initial region span: 1-37,66-185Gap history (edge excluded): 37-66


Alt. candidates: [], []                                                                                   


Model 1BP/2BP comparison: 1BP vs 2BP: 1.06e-02                                                            


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                               


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 37 1.448788 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 66 4.490891 None None None * * *



Target sequence

, 254_A|G, 299_T|C, 423_G|A, 482_C|T, 510_T|C, 523_A|G, 558_T|C, 584_G|A, 653_G|A, 719_T|C, 773_T|C, 803_A|G, 837_T|C, 872_T|C, 884_A|G, 914_A|G, 953_AC|GT, 1019_T|C, 1175_A|G, 1217_C|T,
1328_T|C, 1513_C|T, 1559_A|G, 1592_T|C, 1616_C|T, 1691_C|T, 1787_T|C, 1815_G|A, 1841_C|T, 1850_T|C, 1946_C|T, 2066_C|T, 2111_T|C, 2375_C|T, 2411_C|T, 2448_T|C, 2504_G|A, 2525_G|A, 2606_C|T,
2654_C|T, 2681_G|A, 2724_T|C, 2739_G|A, 2774_C|T, 2799_T|C, 2879_T|C, 2925_G|A, 2949_C|A, 2969_C|T, 3038_T|C, 3041_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3218_T|A, 3228_T|C,
3254_T|C, 3332_G|A, 3350_G|A, 3425_C|T, 3482_T|C, 3518_C|T, 3534_G|A, 3551_A|G, 3596_G|A, 3671_A|G, 3731_C|T, 3800_C|T, 3812_G|A, 3836_T|C, 3857_C|T, 3881_T|C, 3950_C|T, 3989_T|C, 4013_T|C,
4106_A|G, 4133_A|T, 4199_G|T, 4220_G|A, 4274_G|A, 4325_G|A, 4337_A|G, 4403_A|C, 4409_A|G, 4454_G|A, 4481_G|A, 4499_C|T, 4523_G|A, 4925_G|A, 4934_G|A, 5000_T|C, 5030_C|T, 5060_T|C, 5096_T|C,
5279_A|G, 5369_C|T, 5375_A|G, 5384_C|T, 5387_C|T, 5411_C|T, 5421_C|T, 5423_A|G, 5459_T|C, 5555_C|T, 5591_T|C, 5630_A|G, 5717_C|T, 5801_G|A, 5828_T|C, 5858_C|T, 5864_C|T, 6056_C|T, 6068_A|G,
6143_T|C, 6185_T|C, 6404_C|T, 6419_T|C, 6428_C|T, 6506_A|C, 6539_T|C, 6545_C|T, 6551_T|C, 6608_G|A, 6684_A|C, 6686_G|A, 6807_T|C, 6810_C|T, 6827_T|A, 6839_G|A, 6869_A|G, 6923_C|T, 6926_A|T,
6962_A|G, 6983_A|G, 7046_T|C, 7050_T|C, 7157_C|A, 7220_A|G, 7316_T|C, 7451_A|C, 7499_T|C, 7517_C|T, 7586_T|C, 7598_G|A, 7633_T|C, 7637_A|G, 7805_T|C, 7808_T|C, 7880_G|A, 7887_T|C, 7964_A|G,
8007_G|A, 8018_A|G, 8063_C|T, 8069_T|C, 8303_C|G, 8348_C|T, 8408_T|C, 8414_G|A, 8438_G|A, 8465_G|A, 8474_C|T, 8511_A|G, 8591_A|G, 8631_A|G, 8780_T|C, 8804_T|C, 9011_C|T, 9017_T|C, 9038_A|G,
9233_G|A, 9239_T|C, 9305_C|T, 9353_T|C, 9434_A|G, 9455_G|A, 9515_C|T, 9656_T|C, 9992_A|G, 10052_T|C, 10091_T|C, 10163_T|C, 10322_C|T
 Case 3 (A.1): PQ551086.1




Target: 995 samples       Number of changes: 214                                                 


BC: A.1 + A.1             BC BR: 5-6                     BC BR coord: 427 - 428           


Direction L1: <<          Initial region span: 1-5,15-214Gap history (edge excluded): 5-15


Alt. candidates: [], []                                                                                 


Model 1BP/2BP comparison: 1BP vs 2BP: 1.26e-03                                                          


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                             


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 5 0.823532 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 15 9.120325 None None None * * *



Target sequence

, 50_A|G, 188_T|C, 254_A|G, 299_T|C, 423_G|A, 523_A|G, 545_T|C, 558_T|C, 578_T|C, 617_C|T, 653_G|A, 719_T|C, 773_T|C, 803_A|G, 884_A|G, 947_C|T, 953_AC|GT, 968_G|A, 1175_A|G, 1358_G|A,
1482_A|G, 1559_A|G, 1568_C|T, 1616_C|T, 1682_C|T, 1727_C|T, 1787_T|C, 1815_G|A, 1874_A|G, 2015_G|A, 2019_G|A, 2051_G|A, 2066_C|T, 2123_T|C, 2150_C|T, 2375_C|T, 2385_A|G, 2394_A|T, 2411_C|T,
2429_T|C, 2448_T|C, 2486_T|C, 2495_G|A, 2504_G|A, 2525_G|A, 2555_T|C, 2591_C|T, 2606_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2739_G|A, 2774_C|T, 2826_C|T, 2831_C|T, 2879_T|C, 2925_G|A, 2930_T|C,
2949_C|A, 2969_C|T, 2984_T|C, 3017_A|T, 3038_T|C, 3041_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3209_T|C, 3218_T|A, 3228_T|C, 3254_T|C, 3273_A|T, 3332_G|A, 3338_T|C, 3476_T|C,
3518_C|T, 3534_G|A, 3566_T|C, 3584_G|A, 3596_G|A, 3615_C|T, 3644_C|T, 3671_A|G, 3731_C|T, 3836_T|C, 3857_C|T, 3861_C|T, 3881_T|C, 3989_T|C, 3998_C|T, 4070_T|C, 4079_G|A, 4083_T|C, 4085_T|C,
4106_A|G, 4133_A|T, 4220_G|A, 4322_C|T, 4337_A|G, 4346_T|C, 4403_A|C, 4409_A|G, 4451_G|A, 4454_G|A, 4463_G|A, 4484_G|A, 4499_C|T, 4523_G|A, 4631_T|C, 4667_C|T, 4688_A|G, 4733_T|C, 4925_G|A,
4934_G|A, 4938_A|G, 5096_T|C, 5187_T|C, 5256_A|G, 5279_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5390_C|T, 5421_C|T, 5450_T|C, 5459_T|C, 5516_T|C, 5555_C|T, 5561_C|T, 5591_T|C, 5642_A|G, 5717_C|T,
5937_T|C, 5939_G|A, 5975_C|T, 6002_T|C, 6056_C|T, 6101_T|C, 6143_T|C, 6149_C|T, 6363_C|T, 6545_C|T, 6599_G|A, 6684_A|C, 6807_T|C, 6827_T|A, 6839_G|A, 6920_A|G, 6983_A|G, 7050_T|C, 7151_T|C,
7217_C|T, 7226_A|G, 7259_G|A, 7316_T|C, 7517_C|T, 7541_C|T, 7568_T|C, 7598_G|A, 7633_T|C, 7637_A|G, 7766_C|T, 7805_T|C, 7808_T|C, 7973_A|G, 7975_A|T, 7988_C|T, 7994_T|C, 8007_G|A, 8018_A|G,
8063_C|T, 8069_T|C, 8213_A|G, 8255_G|A, 8288_C|T, 8303_C|T, 8312_T|C, 8408_T|C, 8474_C|T, 8504_T|C, 8588_T|C, 8591_A|G, 8606_C|T, 8631_A|G, 8720_T|C, 8780_T|C, 8789_T|C, 8834_C|T, 8849_C|T,
8933_T|C, 8993_C|T, 9194_A|G, 9211_G|A, 9221_T|C, 9239_T|C, 9305_C|T, 9308_T|C, 9329_C|T, 9346_A|G, 9353_T|C, 9434_A|G, 9455_G|A, 9515_C|T, 9869_T|C, 9912_AG|GC, 10027_T|C, 10178_C|T,
10322_C|T, 10361_T|C, 10372_T|C, 10376_G|A, 10392_A|G
 Case 3 (A.1): PQ551087.1




Target: 995 samples       Number of changes: 219                                                       


BC: A.1 + A.1             BC BR: 120-121                    BC BR coord: 5287 - 5288            


Direction L1: <<          Initial region span: 1-104,155-219Gap history (edge excluded): 104-155


Alt. candidates: [], []                                                                                       


Model 1BP/2BP comparison: 1BP vs 2BP: 1.49e-24                                                                


Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00                                                   


Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 104 2.871103 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 155 7.172924 None None None * * *



Target sequence

, 50_A|G, 188_T|C, 254_A|G, 299_T|C, 423_G|A, 523_A|G, 545_T|C, 558_T|C, 578_T|C, 617_C|T, 653_G|A, 719_T|C, 773_T|C, 803_A|G, 884_A|G, 947_C|T, 953_AC|GT, 968_G|A, 1175_A|G, 1358_G|A,
1482_A|G, 1559_A|G, 1568_C|T, 1616_C|T, 1682_C|T, 1727_C|T, 1787_T|C, 1815_G|A, 1874_A|G, 2015_G|A, 2019_G|A, 2051_G|A, 2066_C|T, 2123_T|C, 2375_C|T, 2385_A|G, 2394_A|T, 2411_C|T, 2429_T|C,
2448_T|C, 2486_T|C, 2495_G|A, 2504_G|A, 2525_G|A, 2555_T|C, 2591_C|T, 2606_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2739_G|A, 2774_C|T, 2826_C|T, 2879_T|C, 2925_G|A, 2930_T|C, 2949_C|A, 2969_C|T,
2984_T|C, 3017_A|T, 3038_T|C, 3041_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3209_T|C, 3218_T|A, 3228_T|C, 3254_T|C, 3332_G|A, 3338_T|C, 3476_T|C, 3518_C|T, 3534_G|A, 3566_T|C,
3584_G|A, 3596_G|A, 3615_C|T, 3644_C|T, 3671_A|G, 3731_C|T, 3836_T|C, 3857_C|T, 3861_C|T, 3881_T|C, 3989_T|C, 3998_C|T, 4079_G|A, 4083_T|C, 4085_T|C, 4106_A|G, 4133_A|T, 4220_G|A, 4322_C|T,
4337_A|G, 4403_A|C, 4409_A|G, 4451_G|A, 4454_G|A, 4463_G|A, 4484_G|A, 4499_C|T, 4523_G|A, 4631_T|C, 4667_C|T, 4688_A|G, 4733_T|C, 4817_C|T, 4925_G|A, 4934_G|A, 4938_A|G, 5000_T|C, 5030_C|T,
5060_T|C, 5096_T|C, 5187_T|C, 5256_A|G, 5279_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5390_C|T, 5421_C|T, 5450_T|C, 5459_T|C, 5516_T|C, 5555_C|T, 5561_C|T, 5591_T|C, 5642_A|G, 5717_C|T, 5783_T|C,
5789_G|A, 5798_C|T, 5828_T|C, 5937_T|C, 5939_G|A, 5975_C|T, 6002_T|C, 6056_C|T, 6143_T|C, 6149_C|T, 6363_C|T, 6545_C|T, 6599_G|A, 6684_A|C, 6807_T|C, 6827_T|A, 6839_G|A, 6920_A|G, 6983_A|G,
7050_T|C, 7151_T|C, 7217_C|T, 7226_A|G, 7259_G|A, 7316_T|C, 7451_A|C, 7475_G|A, 7502_G|A, 7517_C|T, 7541_C|T, 7568_T|C, 7598_G|A, 7633_T|C, 7637_A|G, 7766_C|T, 7805_T|C, 7808_T|C, 7870_G|A,
7955_A|G, 7964_A|G, 7973_A|G, 7988_C|T, 8007_G|A, 8018_A|G, 8063_C|T, 8069_T|C, 8213_A|G, 8255_G|A, 8288_C|T, 8303_C|T, 8312_T|C, 8408_T|C, 8474_C|T, 8504_T|C, 8588_T|C, 8591_A|G, 8606_C|T,
8631_A|G, 8720_T|C, 8780_T|C, 8789_T|C, 8834_C|T, 8849_C|T, 8933_T|C, 8993_C|T, 9011_C|T, 9017_T|C, 9194_A|G, 9211_G|A, 9239_T|C, 9305_C|T, 9308_T|C, 9329_C|T, 9346_A|G, 9353_T|C, 9434_A|G,
9455_G|A, 9515_C|T, 9788_A|G, 9869_T|C, 9912_AG|GC, 10027_T|C, 10178_C|T, 10322_C|T, 10361_T|C
 Case 3 (A.1): PQ551088.1




Target: 995 samples        Number of changes: 234                                               


BC: A.1 + A.1.NmC1         BC BR: 230-231                    BC BR coord: 10391 - 10392  


Direction L1: >>           Initial region span: 1-230,231-234Gap history (edge excluded):


Alt. candidates: [], []                                                                                


Model 1BP/2BP comparison:  -                                                                           


Rec. model vs L1: 6.22e+03 Rec. model vs L2: 0.00e+00                                           


Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 995 230 7.106736 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 181 231 3.420355 None None None * * *



Target sequence

, 50_A|G, 80, 188_T|C, 254_A|G, 299_T|C, 423_G|A, 444_G|A, 523_A|G, 545_T|C, 558_T|C, 578_T|C, 617_C|T, 653_G|A, 719_T|C, 773_T|C, 803_A|G, 884_A|G, 947_C|T, 953_AC|GT, 968_G|A, 1175_A|G,
1358_G|A, 1482_A|G, 1559_A|G, 1568_C|T, 1616_C|T, 1682_C|T, 1727_C|T, 1787_T|C, 1815_G|A, 1874_A|G, 2015_G|A, 2019_G|A, 2051_G|A, 2066_C|T, 2123_T|C, 2150_C|T, 2375_C|T, 2385_A|G, 2394_A|T,
2411_C|T, 2429_T|C, 2448_T|C, 2486_T|C, 2495_G|A, 2504_G|A, 2525_G|A, 2555_T|C, 2591_C|T, 2606_C|T, 2654_C|T, 2681_G|A, 2724_T|C, 2739_G|A, 2774_C|T, 2826_C|T, 2831_C|T, 2879_T|C, 2925_G|A,
2930_T|C, 2949_C|A, 2969_C|T, 2984_T|C, 3017_A|T, 3038_T|C, 3041_T|C, 3059_G|A, 3110_T|C, 3137_T|C, 3140_A|G, 3186_G|A, 3209_T|C, 3218_T|A, 3228_T|C, 3254_T|C, 3332_G|A, 3338_T|C, 3476_T|C,
3518_C|T, 3534_G|A, 3566_T|C, 3584_G|A, 3596_G|A, 3615_C|T, 3644_C|T, 3671_A|G, 3674_T|C, 3731_C|T, 3836_T|C, 3857_C|T, 3861_C|T, 3881_T|C, 3989_T|C, 3998_C|T, 4070_T|C, 4079_G|A, 4083_T|C,
4085_T|C, 4106_A|G, 4133_A|T, 4220_G|A, 4322_C|T, 4337_A|G, 4346_T|C, 4403_A|C, 4409_A|G, 4451_G|A, 4454_G|A, 4463_G|A, 4484_G|A, 4499_C|T, 4523_G|A, 4631_T|C, 4667_C|T, 4688_A|G, 4733_T|C,
4817_C|T, 4925_G|A, 4934_G|A, 4938_A|G, 5000_T|C, 5030_C|T, 5060_T|C, 5096_T|C, 5187_T|C, 5256_A|G, 5279_A|G, 5369_C|T, 5375_A|G, 5387_C|T, 5390_C|T, 5421_C|T, 5450_T|C, 5459_T|C, 5516_T|C,
5555_C|T, 5561_C|T, 5591_T|C, 5642_A|G, 5717_C|T, 5783_T|C, 5789_G|A, 5798_C|T, 5828_T|C, 5937_T|C, 5939_G|A, 5975_C|T, 6002_T|C, 6056_C|T, 6143_T|C, 6149_C|T, 6363_C|T, 6545_C|T, 6599_G|A,
6684_A|C, 6807_T|C, 6827_T|A, 6839_G|A, 6920_A|G, 6983_A|G, 7050_T|C, 7151_T|C, 7217_C|T, 7226_A|G, 7259_G|A, 7316_T|C, 7451_A|C, 7475_G|A, 7502_G|A, 7517_C|T, 7541_C|T, 7568_T|C, 7598_G|A,
7633_T|C, 7637_A|G, 7646_C|T, 7766_C|T, 7805_T|C, 7808_T|C, 7880_G|A, 7887_T|C, 7964_A|G, 7973_A|G, 7988_C|T, 8007_G|A, 8018_A|G, 8063_C|T, 8069_T|C, 8213_A|G, 8255_G|A, 8288_C|T, 8303_C|T,
8312_T|C, 8408_T|C, 8474_C|T, 8504_T|C, 8588_T|C, 8591_A|G, 8606_C|T, 8631_A|G, 8720_T|C, 8780_T|C, 8789_T|C, 8834_C|T, 8849_C|T, 8933_T|C, 8993_C|T, 9011_C|T, 9017_T|C, 9194_A|G, 9211_G|A,
9221_T|C, 9239_T|C, 9305_C|T, 9308_T|C, 9329_C|T, 9346_A|G, 9353_T|C, 9434_A|G, 9455_G|A, 9515_C|T, 9869_T|C, 9912_AG|GC, 10027_T|C, 10140_C|T, 10178_C|T, 10322_C|T, 10361_T|C, 10372_T|C,
10376_G|A, 10392_A|G, 10477_T|C, 10561_T|C, 10619_G|A